Library preparation methods and compositions and uses therefor

ABSTRACT

Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.

RELATED APPLICATIONS

This application claims priority to and the benefit under 35 USC § 119(e) of each of U.S. Provisional Application No. 62/527,893 filed Jun. 30, 2017, U.S. Provisional Application No. 62/614,362, filed Jan. 6, 2018, and U.S. Provisional Application No. 62/685,424, filed Jun. 15, 2018. The entire contents of each of the aforementioned applications are herein incorporated by reference in their entirety.

SEQUENCE LISTING

This application hereby incorporates by reference the material of the electronic Sequence Listing filed concurrently herewith. The material in the electronic Sequence Listing is submitted as a text (.txt) file entitled “20180627_LT01273_ST25.txt” created on Jun. 27, 2018 which has a file size of 359 KB and is herein incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to methods of preparing a library of target nucleic acid sequences and compositions and uses therefor.

BRIEF SUMMARY OF THE INVENTION

Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.

One aspect of the invention comprises methods for preparing a library of target nucleic acid sequences. In certain embodiments the methods comprise contacting a nucleic acid sample with a plurality of adaptors wherein each of a pair of adaptors are capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification. The methods further comprise digesting the resulting first amplification products to reduce or eliminate any primer dimers resulting in the reaction and preparing partially digested amplicons, thereby preparing resulting gapped, double stranded partially digested amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired products in a second amplification using universal primers to thereby produce a library of target nucleic acid sequences. Each of the plurality of adaptors used in the provided methods comprise a 5′ universal handle sequence and a 3′ target nucleic acid sequence and a cleavable moiety. Two or more target specific adaptor pairs are included for use in provided methods, wherein each of the 3′ target specific sequences comprise cleavable moieties. Optionally, one or more tag sequences are included.

In another aspect of the invention methods for preparing a library of target nucleic acid sequences having unique tag sequences is provided. In certain embodiments the methods comprise contacting a nucleic acid sample with a plurality of adaptors wherein each of a pair of adaptors are capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification. The methods further comprise digesting the resulting first amplification products to reduce or eliminate any primer dimers resulting in the reaction and preparing partially digested amplicons, thereby preparing resulting gapped, double stranded partially digested amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired products in a second amplification using universal primers to thereby produce a library of target nucleic acid sequences. Each of the plurality of adaptors used in the provided methods comprise a 5′ universal handle sequence, one or more unique tag sequences and a 3′ target nucleic acid sequence and a cleavable moiety. Two or more target specific adaptor pairs are included for use in provided methods, wherein each of the 3′ target specific sequences comprise cleavable moieties, each tag sequence is flanked by cleavable moieties, and each universal handle is without cleavable moieties.

In a further aspect, compositions are provided. In some embodiments provided are compositions comprising nucleic acid libraries generated by the methods described herein. In other embodiments, compositions comprising a plurality of nucleic acid adaptors are provided, wherein each of the plurality of adaptors comprise a 5′ universal handle sequence, one or more unique tag sequences, and a 3′ target nucleic acid sequence wherein each adaptor comprises a cleavable moiety. In certain embodiments the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety. In certain embodiments, compositions include at least two and up to one hundred thousand target specific adaptor pairs.

Still further, uses of provided compositions and kits comprising provided compositions for analysis of sequences of the nucleic acid libraries are additional aspects of the invention. In some embodiments, analysis of the sequences of the resulting libraries enables detection of low frequency alleles in a sample of interest.

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

Efficient methods for production of targeted libraries from complex samples is desirable for a variety of nucleic acid analyses. The present invention provides, inter alia, methods of preparing libraries of target nucleic acid sequences, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences; and resulting library compositions are useful for a variety of applications, including sequencing applications. Novel features of the invention are set forth with particularity in the appended claims; and a complete understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

FIG. 1 depicts a workflow method of the invention that enables efficient rapid, highly multiplexed library preparation.

FIG. 2 depicts results from the experimental description in Example 2A.

FIG. 3 depicts results from the experimental description in Example 2B.

FIG. 4A-4C depicts results from the experimental description in Example 4.

FIG. 5 depicts results from the experimental description in Example 5.

FIG. 6A-6C depicts results from the experimental description in Example 6.

FIG. 7 depicts an additional aspect of the workflow of the invention that enables addition of adaptor sequences to facilitate bidirectional sequencing

FIG. 8 depicts an additional aspect of the workflow of the invention that enables sequencing on Illumina platforms

DESCRIPTION OF THE INVENTION

Section headings used herein are for organizational purposes only and are not to be construed as limiting the described subject matter in any way. All literature and similar materials cited in this application, including but not limited to, patents, patent applications, articles, books, treatises, and internet web pages are expressly incorporated by reference in their entirety for any purpose. When definitions of terms in incorporated references appear to differ from the definitions provided in the present teachings, the definition provided in the present teachings shall control. It will be appreciated that there is an implied “about” prior to the temperatures, concentrations, times, etc discussed in the present teachings, such that slight and insubstantial deviations are within the scope of the present teachings herein. In this application, the use of the singular includes the plural unless specifically stated otherwise. It is noted that, as used in this specification, singular forms “a,” “an,” and “the,” and any singular use of a word, include plural referents unless expressly and unequivocally limited to one referent. Also, the use of “comprise”, “comprises”, “comprising”, “contain”, “contains”, “containing”, “include”, “includes”, and “including” are not intended to be limiting. It is to be understood that both the general description is exemplary and explanatory only and not restrictive of the invention.

Unless otherwise defined, scientific and technical terms used in connection with the invention described herein shall have the meanings that are commonly understood by those of ordinary skill in the art. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. Generally, nomenclatures utilized in connection with, and techniques of, cell and tissue culture, molecular biology, and protein and oligo- or polynucleotide chemistry and hybridization used herein are those well-known and commonly used in the art. Standard techniques are used, for example, for nucleic acid purification and preparation, chemical analysis, recombinant nucleic acid, and oligonucleotide synthesis. Enzymatic reactions and purification techniques are performed according to manufacturer's specifications or as commonly accomplished in the art or as described herein. Techniques and procedures described herein are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the instant specification. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (Third ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 2000). Unless specifically provided, any nomenclature utilized in connection with, and laboratory procedures and techniques described herein are those well-known and commonly used in the art. As utilized in accordance with embodiments provided herein, the following terms, unless otherwise indicated, shall be understood to have the following meanings:

As used herein, “amplify”, “amplifying” or “amplification reaction” and their derivatives, refer generally to an action or process whereby at least a portion of a nucleic acid molecule (referred to as a template nucleic acid molecule) is replicated or copied into at least one additional nucleic acid molecule. The additional nucleic acid molecule optionally includes sequence that is substantially identical or substantially complementary to at least some portion of the template nucleic acid molecule. A template target nucleic acid molecule may be single-stranded or double-stranded. The additional resulting replicated nucleic acid molecule may independently be single-stranded or double-stranded. In some embodiments, amplification includes a template-dependent in vitro enzyme-catalyzed reaction for the production of at least one copy of at least some portion of a target nucleic acid molecule or the production of at least one copy of a target nucleic acid sequence that is complementary to at least some portion of a target nucleic acid molecule. Amplification optionally includes linear or exponential replication of a nucleic acid molecule. In some embodiments, such amplification is performed using isothermal conditions; in other embodiments, such amplification can include thermocycling. In some embodiments, the amplification is a multiplex amplification that includes simultaneous amplification of a plurality of target sequences in a single amplification reaction. At least some target sequences can be situated on the same nucleic acid molecule or on different target nucleic acid molecules included in a single amplification reaction. In some embodiments, “amplification” includes amplification of at least some portion of DNA- and/or RNA-based nucleic acids, whether alone, or in combination. An amplification reaction can include single or double-stranded nucleic acid substrates and can further include any amplification processes known to one of ordinary skill in the art. In some embodiments, an amplification reaction includes polymerase chain reaction (PCR). In some embodiments, an amplification reaction includes isothermal amplification.

As used herein, “amplification conditions” and derivatives (e.g., conditions for amplification, etc.) generally refers to conditions suitable for amplifying one or more nucleic acid sequences. Amplification can be linear or exponential. In some embodiments, amplification conditions include isothermal conditions or alternatively include thermocycling conditions, or a combination of isothermal and thermocycling conditions. In some embodiments, conditions suitable for amplifying one or more target nucleic acid sequences includes polymerase chain reaction (PCR) conditions. Typically, amplification conditions refer to a reaction mixture that is sufficient to amplify nucleic acids such as one or more target sequences, or to amplify an amplified target sequence ligated or attached to one or more adaptors, e.g., an adaptor-attached amplified target sequence. Generally, amplification conditions include a catalyst for amplification or for nucleic acid synthesis, for example a polymerase; a primer that possesses some degree of complementarity to the nucleic acid to be amplified; and nucleotides, such as deoxyribonucleoside triphosphates (dNTPs) to promote extension of a primer once hybridized to a nucleic acid. Amplification conditions can require hybridization or annealing of a primer to a nucleic acid, extension of the primer and a denaturing step in which the extended primer is separated from the nucleic acid sequence undergoing amplification. Typically, though not necessarily, amplification conditions can include thermocycling. In some embodiments, amplification conditions include a plurality of cycles wherein steps of annealing, extending and separating are repeated. Typically, amplification conditions include cations such as Mg⁺⁺ or Mn⁺⁺ (e.g., MgCl₂, etc) and can also optionally include various modifiers of ionic strength.

As used herein, “target sequence” “target nucleic acid sequence” or “target sequence of interest” and derivatives, refers generally to any single or double-stranded nucleic acid sequence that can be amplified or synthesized according to the disclosure, including any nucleic acid sequence suspected or expected to be present in a sample. In some embodiments, the target sequence is present in double-stranded form and includes at least a portion of the particular nucleotide sequence to be amplified or synthesized, or its complement, prior to the addition of target-specific primers or appended adaptors. Target sequences can include the nucleic acids to which primers useful in the amplification or synthesis reaction can hybridize prior to extension by a polymerase. In some embodiments, the term refers to a nucleic acid sequence whose sequence identity, ordering or location of nucleotides is determined by one or more of the methods of the disclosure.

The term “portion” and its variants, as used herein, when used in reference to a given nucleic acid molecule, for example a primer or a template nucleic acid molecule, comprises any number of contiguous nucleotides within the length of the nucleic acid molecule, including the partial or entire length of the nucleic acid molecule.

As used herein, “contacting” and its derivatives, when used in reference to two or more components, refers generally to any process whereby the approach, proximity, mixture or commingling of the referenced components is promoted or achieved without necessarily requiring physical contact of such components, and includes mixing of solutions containing any one or more of the referenced components with each other. The referenced components may be contacted in any particular order or combination and the particular order of recitation of components is not limiting. For example, “contacting A with B and C” encompasses embodiments where A is first contacted with B then C, as well as embodiments where C is contacted with A then B, as well as embodiments where a mixture of A and C is contacted with B, and the like. Furthermore, such contacting does not necessarily require that the end result of the contacting process be a mixture including all of the referenced components, as long as at some point during the contacting process all of the referenced components are simultaneously present or simultaneously included in the same mixture or solution. For example, “contacting A with B and C” can include embodiments wherein C is first contacted with A to form a first mixture, which first mixture is then contacted with B to form a second mixture, following which C is removed from the second mixture; optionally A can then also be removed, leaving only B. Where one or more of the referenced components to be contacted includes a plurality (e.g., “contacting a target sequence with a plurality of target-specific primers and a polymerase”), then each member of the plurality can be viewed as an individual component of the contacting process, such that the contacting can include contacting of any one or more members of the plurality with any other member of the plurality and/or with any other referenced component (e.g., some but not all of the plurality of target specific primers can be contacted with a target sequence, then a polymerase, and then with other members of the plurality of target-specific primers) in any order or combination.

As used herein, the term “primer” and its derivatives refer generally to any polynucleotide that can hybridize to a target sequence of interest. In some embodiments, the primer can also serve to prime nucleic acid synthesis. Typically, a primer functions as a substrate onto which nucleotides can be polymerized by a polymerase; in some embodiments, however, a primer can become incorporated into a synthesized nucleic acid strand and provide a site to which another primer can hybridize to prime synthesis of a new strand that is complementary to the synthesized nucleic acid molecule. A primer may be comprised of any combination of nucleotides or analogs thereof, which may be optionally linked to form a linear polymer of any suitable length. In some embodiments, a primer is a single-stranded oligonucleotide or polynucleotide. (For purposes of this disclosure, the terms ‘polynucleotide” and “oligonucleotide” are used interchangeably herein and do not necessarily indicate any difference in length between the two). In some embodiments, a primer is double-stranded. If double stranded, a primer is first treated to separate its strands before being used to prepare extension products. Preferably, the primer is an oligodeoxyribonucleotide. A primer must be sufficiently long to prime the synthesis of extension products. Lengths of the primers will depend on many factors, including temperature, source of primer and the use of the method. In some embodiments, a primer acts as a point of initiation for amplification or synthesis when exposed to amplification or synthesis conditions; such amplification or synthesis can occur in a template-dependent fashion and optionally results in formation of a primer extension product that is complementary to at least a portion of the target sequence. Exemplary amplification or synthesis conditions can include contacting the primer with a polynucleotide template (e.g., a template including a target sequence), nucleotides and an inducing agent such as a polymerase at a suitable temperature and pH to induce polymerization of nucleotides onto an end of the target-specific primer. If double-stranded, the primer can optionally be treated to separate its strands before being used to prepare primer extension products. In some embodiments, the primer is an oligodeoxyribonucleotide or an oligoribonucleotide. In some embodiments, the primer can include one or more nucleotide analogs. The exact length and/or composition, including sequence, of the target-specific primer can influence many properties, including melting temperature (Tm), GC content, formation of secondary structures, repeat nucleotide motifs, length of predicted primer extension products, extent of coverage across a nucleic acid molecule of interest, number of primers present in a single amplification or synthesis reaction, presence of nucleotide analogs or modified nucleotides within the primers, and the like. In some embodiments, a primer can be paired with a compatible primer within an amplification or synthesis reaction to form a primer pair consisting or a forward primer and a reverse primer. In some embodiments, the forward primer of the primer pair includes a sequence that is substantially complementary to at least a portion of a strand of a nucleic acid molecule, and the reverse primer of the primer of the primer pair includes a sequence that is substantially identical to at least of portion of the strand. In some embodiments, the forward primer and the reverse primer are capable of hybridizing to opposite strands of a nucleic acid duplex. Optionally, the forward primer primes synthesis of a first nucleic acid strand, and the reverse primer primes synthesis of a second nucleic acid strand, wherein the first and second strands are substantially complementary to each other, or can hybridize to form a double-stranded nucleic acid molecule. In some embodiments, one end of an amplification or synthesis product is defined by the forward primer and the other end of the amplification or synthesis product is defined by the reverse primer. In some embodiments, where the amplification or synthesis of lengthy primer extension products is required, such as amplifying an exon, coding region, or gene, several primer pairs can be created than span the desired length to enable sufficient amplification of the region. In some embodiments, a primer can include one or more cleavable groups. In some embodiments, primer lengths are in the range of about 10 to about 60 nucleotides, about 12 to about 50 nucleotides and about 15 to about 40 nucleotides in length. Typically, a primer is capable of hybridizing to a corresponding target sequence and undergoing primer extension when exposed to amplification conditions in the presence of dNTPS and a polymerase. In some instances, the particular nucleotide sequence or a portion of the primer is known at the outset of the amplification reaction or can be determined by one or more of the methods disclosed herein. In some embodiments, the primer includes one or more cleavable groups at one or more locations within the primer.

As used herein, “target-specific primer” and its derivatives, refers generally to a single stranded or double-stranded polynucleotide, typically an oligonucleotide, that includes at least one sequence that is at least 50% complementary, typically at least 75% complementary or at least 85% complementary, more typically at least 90% complementary, more typically at least 95% complementary, more typically at least 98% or at least 99% complementary, or identical, to at least a portion of a nucleic acid molecule that includes a target sequence. In such instances, the target-specific primer and target sequence are described as “corresponding” to each other. In some embodiments, the target-specific primer is capable of hybridizing to at least a portion of its corresponding target sequence (or to a complement of the target sequence); such hybridization can optionally be performed under standard hybridization conditions or under stringent hybridization conditions. In some embodiments, the target-specific primer is not capable of hybridizing to the target sequence, or to its complement, but is capable of hybridizing to a portion of a nucleic acid strand including the target sequence, or to its complement. In some embodiments, the target-specific primer includes at least one sequence that is at least 75% complementary, typically at least 85% complementary, more typically at least 90% complementary, more typically at least 95% complementary, more typically at least 98% complementary, or more typically at least 99% complementary, to at least a portion of the target sequence itself; in other embodiments, the target-specific primer includes at least one sequence that is at least 75% complementary, typically at least 85% complementary, more typically at least 90% complementary, more typically at least 95% complementary, more typically at least 98% complementary, or more typically at least 99% complementary, to at least a portion of the nucleic acid molecule other than the target sequence. In some embodiments, the target-specific primer is substantially non-complementary to other target sequences present in the sample; optionally, the target-specific primer is substantially non-complementary to other nucleic acid molecules present in the sample. In some embodiments, nucleic acid molecules present in the sample that do not include or correspond to a target sequence (or to a complement of the target sequence) are referred to as “non-specific” sequences or “non-specific nucleic acids”. In some embodiments, the target-specific primer is designed to include a nucleotide sequence that is substantially complementary to at least a portion of its corresponding target sequence. In some embodiments, a target-specific primer is at least 95% complementary, or at least 99% complementary, or identical, across its entire length to at least a portion of a nucleic acid molecule that includes its corresponding target sequence. In some embodiments, a target-specific primer can be at least 90%, at least 95% complementary, at least 98% complementary or at least 99% complementary, or identical, across its entire length to at least a portion of its corresponding target sequence. In some embodiments, a forward target-specific primer and a reverse target-specific primer define a target-specific primer pair that can be used to amplify the target sequence via template-dependent primer extension. Typically, each primer of a target-specific primer pair includes at least one sequence that is substantially complementary to at least a portion of a nucleic acid molecule including a corresponding target sequence but that is less than 50% complementary to at least one other target sequence in the sample. In some embodiments, amplification can be performed using multiple target-specific primer pairs in a single amplification reaction, wherein each primer pair includes a forward target-specific primer and a reverse target-specific primer, each including at least one sequence that substantially complementary or substantially identical to a corresponding target sequence in the sample, and each primer pair having a different corresponding target sequence. In some embodiments, the target-specific primer can be substantially non-complementary at its 3′ end or its 5′ end to any other target-specific primer present in an amplification reaction. In some embodiments, the target-specific primer can include minimal cross hybridization to other target-specific primers in the amplification reaction. In some embodiments, target-specific primers include minimal cross-hybridization to non-specific sequences in the amplification reaction mixture. In some embodiments, the target-specific primers include minimal self-complementarity. In some embodiments, the target-specific primers can include one or more cleavable groups located at the 3′ end. In some embodiments, the target-specific primers can include one or more cleavable groups located near or about a central nucleotide of the target-specific primer. In some embodiments, one of more targets-specific primers includes only non-cleavable nucleotides at the 5′ end of the target-specific primer. In some embodiments, a target specific primer includes minimal nucleotide sequence overlap at the 3′ end or the 5′ end of the primer as compared to one or more different target-specific primers, optionally in the same amplification reaction. In some embodiments 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, target-specific primers in a single reaction mixture include one or more of the above embodiments. In some embodiments, substantially all of the plurality of target-specific primers in a single reaction mixture includes one or more of the above embodiments.

As used herein, the term “adaptor” denotes a nucleic acid molecule that can be used for manipulation of a polynucleotide of interest. In some embodiments, adaptors are used for amplification of one or more target nucleic acids. In some embodiments, the adaptors are used in reactions for sequencing. In some embodiments, an adaptor has one or more ends that lack a 5′ phosphate residue. In some embodiments, an adaptor comprises, consists of, or consist essentially of at least one priming site. Such priming site containing adaptors can be referred to as “primer” adaptors. In some embodiments, the adaptor priming site can be useful in PCR processes. In some embodiments an adaptor includes a nucleic acid sequence that is substantially complementary to the 3′ end or the 5′ end of at least one target sequences within the sample, referred to herein as a gene specific target sequence, a target specific sequence, or target specific primer. In some embodiments, the adaptor includes nucleic acid sequence that is substantially non-complementary to the 3′ end or the 5′ end of any target sequence present in the sample. In some embodiments, the adaptor includes single stranded or double-stranded linear oligonucleotide that is not substantially complementary to an target nucleic acid sequence. In some embodiments, the adaptor includes nucleic acid sequence that is substantially non-complementary to at least one, and preferably some or all of the nucleic acid molecules of the sample. In some embodiments, suitable adaptor lengths are in the range of about 10-75 nucleotides, about 12-50 nucleotides and about 15-40 nucleotides in length. Generally, an adaptor can include any combination of nucleotides and/or nucleic acids. In some aspects, adaptors include one or more cleavable groups at one or more locations. In some embodiments, the adaptor includes sequence that is substantially identical, or substantially complementary, to at least a portion of a primer, for example a universal primer. In some embodiments, adaptors include a tag sequence to assist with cataloguing, identification or sequencing. In some embodiments, an adaptor acts as a substrate for amplification of a target sequence, particularly in the presence of a polymerase and dNTPs under suitable temperature and pH.

As used herein, “polymerase” and its derivatives, generally refers to any enzyme that can catalyze the polymerization of nucleotides (including analogs thereof) into a nucleic acid strand. Typically but not necessarily, such nucleotide polymerization can occur in a template-dependent fashion. Such polymerases can include without limitation naturally occurring polymerases and any subunits and truncations thereof, mutant polymerases, variant polymerases, recombinant, fusion or otherwise engineered polymerases, chemically modified polymerases, synthetic molecules or assemblies, and any analogs, derivatives or fragments thereof that retain the ability to catalyze such polymerization. Optionally, the polymerase can be a mutant polymerase comprising one or more mutations involving the replacement of one or more amino acids with other amino acids, the insertion or deletion of one or more amino acids from the polymerase, or the linkage of parts of two or more polymerases. Typically, the polymerase comprises one or more active sites at which nucleotide binding and/or catalysis of nucleotide polymerization can occur. Some exemplary polymerases include without limitation DNA polymerases and RNA polymerases. The term “polymerase” and its variants, as used herein, also refers to fusion proteins comprising at least two portions linked to each other, where the first portion comprises a peptide that can catalyze the polymerization of nucleotides into a nucleic acid strand and is linked to a second portion that comprises a second polypeptide. In some embodiments, the second polypeptide can include a reporter enzyme or a processivity-enhancing domain. Optionally, the polymerase can possess 5′ exonuclease activity or terminal transferase activity. In some embodiments, the polymerase can be optionally reactivated, for example through the use of heat, chemicals or re-addition of new amounts of polymerase into a reaction mixture. In some embodiments, the polymerase can include a hot-start polymerase and/or an aptamer based polymerase that optionally can be reactivated.

The terms “identity” and “identical” and their variants, as used herein, when used in reference to two or more nucleic acid sequences, refer to similarity in sequence of the two or more sequences (e.g., nucleotide or polypeptide sequences). In the context of two or more homologous sequences, the percent identity or homology of the sequences or subsequences thereof indicates the percentage of all monomeric units (e.g., nucleotides or amino acids) that are the same (i.e., about 70% identity, preferably 75%, 80%, 85%, 90%, 95%, 98% or 99% identity). The percent identity can be over a specified region, when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection. Sequences are said to be “substantially identical” when there is at least 85% identity at the amino acid level or at the nucleotide level. Preferably, the identity exists over a region that is at least about 25, 50, or 100 residues in length, or across the entire length of at least one compared sequence. A typical algorithm for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al, Nuc. Acids Res. 25:3389-3402 (1977). Other methods include the algorithms of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), and Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), etc. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent hybridization conditions.

The terms “complementary” and “complement” and their variants, as used herein, refer to any two or more nucleic acid sequences (e.g., portions or entireties of template nucleic acid molecules, target sequences and/or primers) that can undergo cumulative base pairing at two or more individual corresponding positions in antiparallel orientation, as in a hybridized duplex. Such base pairing can proceed according to any set of established rules, for example according to Watson-Crick base pairing rules or according to some other base pairing paradigm. Optionally there can be “complete” or “total” complementarity between a first and second nucleic acid sequence where each nucleotide in the first nucleic acid sequence can undergo a stabilizing base pairing interaction with a nucleotide in the corresponding antiparallel position on the second nucleic acid sequence. “Partial” complementarity describes nucleic acid sequences in which at least 20%, but less than 100%, of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. In some embodiments, at least 50%, but less than 100%, of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. In some embodiments, at least 70%, 80%, 90%, 95% or 98%, but less than 100%, of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. Sequences are said to be “substantially complementary” when at least 85% of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. In some embodiments, two complementary or substantially complementary sequences are capable of hybridizing to each other under standard or stringent hybridization conditions. “Non-complementary” describes nucleic acid sequences in which less than 20% of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. Sequences are said to be “substantially non-complementary” when less than 15% of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. In some embodiments, two non-complementary or substantially non-complementary sequences cannot hybridize to each other under standard or stringent hybridization conditions. A “mismatch” is present at any position in the two opposed nucleotides are not complementary. Complementary nucleotides include nucleotides that are efficiently incorporated by DNA polymerases opposite each other during DNA replication under physiological conditions. In a typical embodiment, complementary nucleotides can form base pairs with each other, such as the A-T/U and G-C base pairs formed through specific Watson-Crick type hydrogen bonding, or base pairs formed through some other type of base pairing paradigm, between the nucleobases of nucleotides and/or polynucleotides in positions antiparallel to each other. The complementarity of other artificial base pairs can be based on other types of hydrogen bonding and/or hydrophobicity of bases and/or shape complementarity between bases.

As used herein, “amplified target sequences” and its derivatives, refers generally to a nucleic acid sequence produced by the amplification of/amplifying the target sequences using target-specific primers and the methods provided herein. The amplified target sequences may be either of the same sense (the positive strand produced in the second round and subsequent even-numbered rounds of amplification) or antisense (i.e., the negative strand produced during the first and subsequent odd-numbered rounds of amplification) with respect to the target sequences. For the purposes of this disclosure, amplified target sequences are typically less than 50% complementary to any portion of another amplified target sequence in the reaction.

As used herein, terms “ligating”, “ligation” and derivatives refer generally to the act or process for covalently linking two or more molecules together, for example, covalently linking two or more nucleic acid molecules to each other. In some embodiments, ligation includes joining nicks between adjacent nucleotides of nucleic acids. In some embodiments, ligation includes forming a covalent bond between an end of a first and an end of a second nucleic acid molecule. In some embodiments, for example embodiments wherein the nucleic acid molecules to be ligated include conventional nucleotide residues, the ligation can include forming a covalent bond between a 5′ phosphate group of one nucleic acid and a 3′ hydroxyl group of a second nucleic acid thereby forming a ligated nucleic acid molecule. In some embodiments, any means for joining nicks or bonding a 5′phosphate to a 3′ hydroxyl between adjacent nucleotides can be employed. In an exemplary embodiment, an enzyme such as a ligase can be used.

As used herein, “ligase” and its derivatives, refers generally to any agent capable of catalyzing the ligation of two substrate molecules. In some embodiments, the ligase includes an enzyme capable of catalyzing the joining of nicks between adjacent nucleotides of a nucleic acid. In some embodiments, a ligase includes an enzyme capable of catalyzing the formation of a covalent bond between a 5′ phosphate of one nucleic acid molecule to a 3′ hydroxyl of another nucleic acid molecule thereby forming a ligated nucleic acid molecule. Suitable ligases may include, but not limited to, T4 DNA ligase; T7 DNA ligase; Taq DNA ligase, and E. coli DNA ligase.

As defined herein, a “cleavable group” generally refers to any moiety that once incorporated into a nucleic acid can be cleaved under appropriate conditions. For example, a cleavable group can be incorporated into a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample. In an exemplary embodiment, a target-specific primer can include a cleavable group that becomes incorporated into the amplified product and is subsequently cleaved after amplification, thereby removing a portion, or all, of the target-specific primer from the amplified product. The cleavable group can be cleaved or otherwise removed from a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample by any acceptable means. For example, a cleavable group can be removed from a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample by enzymatic, thermal, photo-oxidative or chemical treatment. In one aspect, a cleavable group can include a nucleobase that is not naturally occurring. For example, an oligodeoxyribonucleotide can include one or more RNA nucleobases, such as uracil that can be removed by a uracil glycosylase. In some embodiments, a cleavable group can include one or more modified nucleobases (such as 7-methylguanine, 8-oxo-guanine, xanthine, hypoxanthine, 5,6-dihydrouracil or 5-methylcytosine) or one or more modified nucleosides (i.e., 7-methylguanosine, 8-oxo-deoxyguanosine, xanthosine, inosine, dihydrouridine or 5-methylcytidine). The modified nucleobases or nucleotides can be removed from the nucleic acid by enzymatic, chemical or thermal means. In one embodiment, a cleavable group can include a moiety that can be removed from a primer after amplification (or synthesis) upon exposure to ultraviolet light (i.e., bromodeoxyuridine). In another embodiment, a cleavable group can include methylated cytosine. Typically, methylated cytosine can be cleaved from a primer for example, after induction of amplification (or synthesis), upon sodium bisulfite treatment. In some embodiments, a cleavable moiety can include a restriction site. For example, a primer or target sequence can include a nucleic acid sequence that is specific to one or more restriction enzymes, and following amplification (or synthesis), the primer or target sequence can be treated with the one or more restriction enzymes such that the cleavable group is removed. Typically, one or more cleavable groups can be included at one or more locations with a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample.

As used herein, “digestion”, “digestion step” and its derivatives, generally refers to any process by which a cleavable group is cleaved or otherwise removed from a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample. In some embodiments, the digestion step involves a chemical, thermal, photo-oxidative or digestive process.

As used herein, the term “hybridization” is consistent with its use in the art, and generally refers to the process whereby two nucleic acid molecules undergo base pairing interactions. Two nucleic acid molecule molecules are said to be hybridized when any portion of one nucleic acid molecule is base paired with any portion of the other nucleic acid molecule; it is not necessarily required that the two nucleic acid molecules be hybridized across their entire respective lengths and in some embodiments, at least one of the nucleic acid molecules can include portions that are not hybridized to the other nucleic acid molecule. The phrase “hybridizing under stringent conditions” and its variants refers generally to conditions under which hybridization of a target-specific primer to a target sequence occurs in the presence of high hybridization temperature and low ionic strength. As used herein, the phrase “standard hybridization conditions” and its variants refers generally to conditions under which hybridization of a primer to an oligonucleotide (i.e., a target sequence), occurs in the presence of low hybridization temperature and high ionic strength. In one exemplary embodiment, standard hybridization conditions include an aqueous environment containing about 100 mm magnesium sulfate, about 500 mM Tris-sulfate at pH 8.9, and about 200 mM ammonium sulfate at about 50-55° C., or equivalents thereof.

As used herein, the term “end” and its variants, when used in reference to a nucleic acid molecule, for example a target sequence or amplified target sequence, can include the terminal 30 nucleotides, the terminal 20 and even more typically the terminal 15 nucleotides of the nucleic acid molecule. A linear nucleic acid molecule comprised of linked series of contiguous nucleotides typically includes at least two ends. In some embodiments, one end of the nucleic acid molecule can include a 3′ hydroxyl group or its equivalent, and can be referred to as the “3′ end” and its derivatives. Optionally, the 3′ end includes a 3′ hydroxyl group that is not linked to a 5′ phosphate group of a mononucleotide pentose ring. Typically, the 3′ end includes one or more 5′ linked nucleotides located adjacent to the nucleotide including the unlinked 3′ hydroxyl group, typically the 30 nucleotides located adjacent to the 3′ hydroxyl, typically the terminal 20 and even more typically the terminal 15 nucleotides. Generally, the one or more linked nucleotides can be represented as a percentage of the nucleotides present in the oligonucleotide or can be provided as a number of linked nucleotides adjacent to the unlinked 3′ hydroxyl. For example, the 3′ end can include less than 50% of the nucleotide length of the oligonucleotide. In some embodiments, the 3′ end does not include any unlinked 3′ hydroxyl group but can include any moiety capable of serving as a site for attachment of nucleotides via primer extension and/or nucleotide polymerization. In some embodiments, the term “3′ end” for example when referring to a target-specific primer, can include the terminal 10 nucleotides, the terminal 5 nucleotides, the terminal 4, 3, 2 or fewer nucleotides at the 3′end. In some embodiments, the term “3′ end” when referring to a target-specific primer can include nucleotides located at nucleotide positions 10 or fewer from the 3′ terminus. As used herein, “5′ end”, and its derivatives, generally refers to an end of a nucleic acid molecule, for example a target sequence or amplified target sequence, which includes a free 5′ phosphate group or its equivalent. In some embodiments, the 5′ end includes a 5′ phosphate group that is not linked to a 3′ hydroxyl of a neighboring mononucleotide pentose ring. Typically, the 5′ end includes to one or more linked nucleotides located adjacent to the 5′ phosphate, typically the 30 nucleotides located adjacent to the nucleotide including the 5′ phosphate group, typically the terminal 20 and even more typically the terminal 15 nucleotides. Generally, the one or more linked nucleotides can be represented as a percentage of the nucleotides present in the oligonucleotide or can be provided as a number of linked nucleotides adjacent to the 5′ phosphate. For example, the 5′ end can be less than 50% of the nucleotide length of an oligonucleotide. In another exemplary embodiment, the 5′ end can include about 15 nucleotides adjacent to the nucleotide including the terminal 5′ phosphate. In some embodiments, the 5′ end does not include any unlinked 5′ phosphate group but can include any moiety capable of serving as a site of attachment to a 3′ hydroxyl group, or to the 3′end of another nucleic acid molecule. In some embodiments, the term “5′ end” for example when referring to a target-specific primer, can include the terminal 10 nucleotides, the terminal 5 nucleotides, the terminal 4, 3, 2 or fewer nucleotides at the 5′end. In some embodiments, the term “5′ end” when referring to a target-specific primer can include nucleotides located at positions 10 or fewer from the 5′ terminus. In some embodiments, the 5′ end of a target-specific primer can include only non-cleavable nucleotides, for example nucleotides that do not contain one or more cleavable groups as disclosed herein, or a cleavable nucleotide as would be readily determined by one of ordinary skill in the art. A “first end” and a “second end” of a polynucleotide refer to the 5′ end or the 3′end of the polynucleotide. Either the first end or second end of a polynucleotide can be the 5′ end or the 3′ end of the polynucleotide; the terms “first” and “second” are not meant to denote that the end is specifically the 5′ end or the 3′ end.

As used herein “tag,” “barcode,” “unique tag” or “tag sequence” and its derivatives, refers generally to a unique short (6-14 nucleotide) nucleic acid sequence within an adaptor or primer that can act as a ‘key’ to distinguish or separate a plurality of amplified target sequences in a sample. For the purposes of this disclosure, a barcode or unique tag sequence is incorporated into the nucleotide sequence of an adaptor or primer. As used herein, “barcode sequence” denotes a nucleic acid fixed sequence that is sufficient to allow for the identification of a sample or source of nucleic acid sequences of interest. A barcode sequence can be, but need not be, a small section of the original nucleic acid sequence on which the identification is to be based. In some embodiments a barcode is 5-20 nucleic acids long. In some embodiments, the barcode is comprised of analog nucleotides, such as L-DNA, LNA, PNA, etc. As used herein, “unique tag sequence” denotes a nucleic acid sequence having at least one random sequence and at least one fixed sequence. A unique tag sequence, alone or in conjunction with a second unique tag sequence, is sufficient to allow for the identification of a single target nucleic acid molecule in a sample. A unique tag sequence can, but need not, comprise a small section of the original target nucleic acid sequence. In some embodiments a unique tag sequence is 2-50 nucleotides or base-pairs, or 2-25 nucleotides or base-pairs, or 2-10 nucleotides or base-pairs in length. A unique tag sequence can comprise at least one random sequence interspersed with a fixed sequence.

As used herein, “comparable maximal minimum melting temperatures” and its derivatives, refers generally to the melting temperature (Tm) of each nucleic acid fragment for a single adaptor or target-specific primer after digestion of a cleavable groups. The hybridization temperature of each nucleic acid fragment generated by an adaptor or target-specific primer is compared to determine the maximal minimum temperature required preventing hybridization of a nucleic acid sequence from the target-specific primer or adaptor or fragment or portion thereof to a respective target sequence. Once the maximal hybridization temperature is known, it is possible to manipulate the adaptor or target-specific primer, for example by moving the location of one or more cleavable group(s) along the length of the primer, to achieve a comparable maximal minimum melting temperature with respect to each nucleic acid fragment to thereby optimize digestion and repair steps of library preparation.

As used herein, “addition only” and its derivatives, refers generally to a series of steps in which reagents and components are added to a first or single reaction mixture. Typically, the series of steps excludes the removal of the reaction mixture from a first vessel to a second vessel in order to complete the series of steps. Generally, an addition only process excludes the manipulation of the reaction mixture outside the vessel containing the reaction mixture. Typically, an addition-only process is amenable to automation and high-throughput.

As used herein, “polymerizing conditions” and its derivatives, refers generally to conditions suitable for nucleotide polymerization. In typical embodiments, such nucleotide polymerization is catalyzed by a polymerase. In some embodiments, polymerizing conditions include conditions for primer extension, optionally in a template-dependent manner, resulting in the generation of a synthesized nucleic acid sequence. In some embodiments, the polymerizing conditions include polymerase chain reaction (PCR). Typically, the polymerizing conditions include use of a reaction mixture that is sufficient to synthesize nucleic acids and includes a polymerase and nucleotides. The polymerizing conditions can include conditions for annealing of a target-specific primer to a target sequence and extension of the primer in a template dependent manner in the presence of a polymerase. In some embodiments, polymerizing conditions can be practiced using thermocycling. Additionally, polymerizing conditions can include a plurality of cycles where the steps of annealing, extending, and separating the two nucleic strands are repeated. Typically, the polymerizing conditions include a cation such as MgCl₂. Generally, polymerization of one or more nucleotides to form a nucleic acid strand includes that the nucleotides be linked to each other via phosphodiester bonds, however, alternative linkages may be possible in the context of particular nucleotide analogs.

As used herein, the term “nucleic acid” refers to natural nucleic acids, artificial nucleic acids, analogs thereof, or combinations thereof, including polynucleotides and oligonucleotides. As used herein, the terms “polynucleotide” and “oligonucleotide” are used interchangeably and mean single-stranded and double-stranded polymers of nucleotides including, but not limited to, 2′-deoxyribonucleotides (nucleic acid) and ribonucleotides (RNA) linked by internucleotide phosphodiester bond linkages, e.g. 3′-5′ and 2′-5′, inverted linkages, e.g. 3′-3′ and 5′-5′, branched structures, or analog nucleic acids. Polynucleotides have associated counter ions, such as H⁺, NH₄ ⁺, trialkylammonium, Mg²⁺, Na⁺ and the like. An oligonucleotide can be composed entirely of deoxyribonucleotides, entirely of ribonucleotides, or chimeric mixtures thereof. Oligonucleotides can be comprised of nucleobase and sugar analogs. Polynucleotides typically range in size from a few monomeric units, e.g. 5-40, when they are more commonly frequently referred to in the art as oligonucleotides, to several thousands of monomeric nucleotide units, when they are more commonly referred to in the art as polynucleotides; for purposes of this disclosure, however, both oligonucleotides and polynucleotides may be of any suitable length. Unless denoted otherwise, whenever a oligonucleotide sequence is represented, it will be understood that the nucleotides are in 5′ to 3′ order from left to right and that “A” denotes deoxyadenosine, “C” denotes deoxycytidine, “G” denotes deoxyguanosine, “T” denotes thymidine, and “U’ denotes deoxyuridine. As discussed herein and known in the art, oligonucleotides and polynucleotides are said to have “5′ ends” and “3′ ends” because mononucleotides are typically reacted to form oligonucleotides via attachment of the 5′ phosphate or equivalent group of one nucleotide to the 3′ hydroxyl or equivalent group of its neighboring nucleotide, optionally via a phosphodiester or other suitable linkage.

As used herein, the term “polymerase chain reaction” (“PCR”) refers to the method of K. B. Mullis U.S. Pat. Nos. 4,683,195 and 4,683,202, hereby incorporated by reference, which describe a method for increasing the concentration of a segment of a polynucleotide of interest in a mixture of genomic DNA without cloning or purification. This process for amplifying the polynucleotide of interest consists of introducing a large excess of two oligonucleotide primers to the DNA mixture containing the desired polynucleotide of interest, followed by a precise sequence of thermal cycling in the presence of a DNA polymerase. The two primers are complementary to their respective strands of the double stranded polynucleotide of interest. To effect amplification, the mixture is denatured and the primers then annealed to their complementary sequences within the polynucleotide of interest molecule. Following annealing, the primers are extended with a polymerase to form a new pair of complementary strands. The steps of denaturation, primer annealing and polymerase extension can be repeated many times (i.e., denaturation, annealing and extension constitute one “cycle”; there can be numerous “cycles”) to obtain a high concentration of an amplified segment of the desired polynucleotide of interest. The length of the amplified segment of the desired polynucleotide of interest (amplicon) is determined by the relative positions of the primers with respect to each other, and therefore, this length is a controllable parameter. By virtue of repeating the process, the method is referred to as the “polymerase chain reaction” (hereinafter “PCR”). Because the desired amplified segments of the polynucleotide of interest become the predominant nucleic acid sequences (in terms of concentration) in the mixture, they are said to be “PCR amplified”. As defined herein, target nucleic acid molecules within a sample including a plurality of target nucleic acid molecules are amplified via PCR. In a modification to the method discussed above, the target nucleic acid molecules can be PCR amplified using a plurality of different primer pairs, in some cases, one or more primer pairs per target nucleic acid molecule of interest, thereby forming a multiplex PCR reaction. Using multiplex PCR, it is possible to simultaneously amplify multiple nucleic acid molecules of interest from a sample to form amplified target sequences. It is also possible to detect the amplified target sequences by several different methodologies (e.g., quantitation with a bioanalyzer or qPCR, hybridization with a labeled probe; incorporation of biotinylated primers followed by avidin-enzyme conjugate detection; incorporation of ³²P-labeled deoxynucleotide triphosphates, such as dCTP or dATP, into the amplified target sequence). Any oligonucleotide sequence can be amplified with the appropriate set of primers, thereby allowing for the amplification of target nucleic acid molecules from genomic DNA, cDNA, formalin-fixed paraffin-embedded DNA, fine-needle biopsies and various other sources. In particular, the amplified target sequences created by the multiplex PCR process as disclosed herein, are themselves efficient substrates for subsequent PCR amplification or various downstream assays or manipulations.

As defined herein “multiplex amplification” refers to selective and non-random amplification of two or more target sequences within a sample using at least one target-specific primer. In some embodiments, multiplex amplification is performed such that some or all of the target sequences are amplified within a single reaction vessel. The “plexy” or “plex” of a given multiplex amplification refers generally to the number of different target-specific sequences that are amplified during that single multiplex amplification. In some embodiments, the plexy can be about 12-plex, 24-plex, 48-plex, 96-plex, 192-plex, 384-plex, 768-plex, 1536-plex, 3072-plex, 6144-plex or higher.

Methods of Preparing Nucleic Acid Libraries

Provided methods of the invention comprise efficient procedures which enable rapid preparation of highly multiplexed libraries suitable for downstream analysis. See FIG. 1. The methods optionally allow for incorporation of one or more unique tag sequences, if so desired. Certain methods comprise streamlined, addition-only procedures conveying highly rapid library generation.

In one aspect of the invention, methods for preparing a library of target nucleic acid sequences are provided. In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

In one aspect of the invention, methods for preparing a tagged library of target nucleic acid sequences are provided. In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and the cleavable moieties are included flanking either end of the tag sequence.

In certain embodiments, the comparable maximal minimum melting temperature of each universal sequence is higher than the comparable maximal minimum melting temperature of each target nucleic acid sequence and each tag sequence present in an adaptor.

In some embodiments, each of the adaptors comprise unique tag sequences as further described herein and each further comprise cleavable groups flanking either end of the tag sequence in each adaptor. In some embodiments wherein unique taq sequences are employed, each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In certain embodiments each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences.

In some embodiments, methods comprise contacting the plurality of gapped polynucleotide products with digestion and repair reagents simultaneously. In some embodiments, methods comprise contacting the plurality of gapped polynucleotide products sequentially with the digestion then repair reagents.

A digestion reagent useful in the methods provided herein comprises any reagent capable of cleaving the cleavable site present in adaptors, and in some embodiments includes, but is not limited to, one or a combination of uracil DNA glycosylase (UDG). apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta.

A repair reagent useful in the methods provided herein comprises any reagent capable of repair of the gapped amplicons, and in some embodiments includes, but is not limited to, any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase.

Thus, in certain embodiments, a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG). apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase.

In some embodiments, methods comprise the digestion and repair steps carried out in a single step. In other embodiments, methods comprise the digestion and repair of steps carried out in a temporally separate manner at different temperatures.

In some embodiments methods of the invention are carried out wherein one or more of the method steps is conducted in manual mode. In particular embodiments, methods of the invention are carried out wherein each of the method steps is conducted manually. In some embodiments methods of the invention are carried out wherein one or more of the method steps is conducted in an automated mode. In particular embodiments, methods of the invention are carried wherein each of the method steps is automated. In some embodiments methods of the invention are carried out wherein one or more of the method steps is conducted in a combination of manual and automated modes.

In some embodiments, methods of the invention comprise at least one purification step. For example, in certain embodiments a purification step is carried out only after the second amplification of repaired amplicons. In some embodiments two purification steps are utilized, wherein a first purification step is carried out after the digestion and repair and a second purification step is carried out after the second amplification of repaired amplicons.

In some embodiments a purification step comprises conducting a solid phase adherence reaction, solid phase immobilization reaction or gel electrophoresis. In certain embodiments a purification step comprises separation conducted using Solid Phase Reversible Immobilization (SPRI) beads. In particular embodiments a purification step comprises separation conducted using SPRI beads wherein the SPRI beads comprise paramagnetic beads.

In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons, then purifying repaired amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; and then purifying resulting library. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons, and purifying repaired amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; and then purifying resulting library. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and cleavable moieties are included in the flanking either end of the tag sequence.

In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons, then purifying repaired amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; and then purifying resulting library. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence. In some embodiments a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG). apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase.

In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons, and purifying repaired amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; and then purifying resulting library. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and cleavable moieties are included in the flanking either end of the tag sequence. In some embodiments a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG). apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase.

In certain embodiments methods of the invention are carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries. For example, in one embodiment, methods for preparing a library of target nucleic acid sequences comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences, and purifying the resulting library. In certain embodiments the purification comprises a single or repeated separating step that is carried out following production of the library following the second amplification; and wherein the other method steps are conducted in a single reaction vessel without requisite transferring of a portion (aliquot) of any of the products generated in steps to another reaction vessel. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

In another embodiment, methods for preparing a tagged library of target nucleic acid sequences are provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences, and purifying the resulting library. In certain embodiments the purification comprises a single or repeated separating step; and wherein the other method steps are optionally conducted in a single reaction vessel without requisite transferring of a portion of any of the products generated in steps to another reaction vessel. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and the cleavable moieties are included flanking either end of the tag sequence.

In one embodiment, methods for preparing a library of target nucleic acid sequences comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicon; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences, and purifying the resulting library.

In some embodiments a digestion reagent comprises any one or any combination of: uracil DNA glycosylase (UDG). AP endonuclease (APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase, Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In certain embodiments a digestion reagent comprises any one or any combination of: uracil DNA glycosylase (UDG). AP endonuclease (APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase, Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta wherein the digestion reagent lacks formamidopyrimidine [fapy]-DNA glycosylase (fpg).

In some embodiments a digestion reagent comprises a single-stranded DNA exonuclease that degrades in a 5′-3′ direction. In some embodiments a cleavage reagent comprises a single-stranded DNA exonuclease that degrades abasic sites. In some embodiments herein the digestions reagent comprises an RecJf exonuclease. In particular embodiments a digestion reagent comprises APE1 and RecJf, wherein the cleavage reagent comprises an apurinic/apyrimidinic endonuclease. In certain embodiments the digestion reagent comprises an AP endonuclease (APE1).

In some embodiments a repair reagent comprises at least one DNA polymerase; wherein the gap-filling reagent comprises: any one or any combination of: Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase and/or SuperFi U DNA polymerase. In some embodiments a repair reagent further comprises a plurality of nucleotides.

In some embodiment a repair reagent comprises an ATP-dependent or an ATP-independent ligase; wherein the repair reagent comprises any one or any combination of: E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase. 9° N DNA ligase

In certain embodiments a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG). apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In particular embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments a purification comprises a single or repeated separating step that is carried out following production of the library following the second amplification; and wherein method steps are conducted in a single reaction vessel without requisite transferring of a portion of any of the products generated in steps to another reaction vessel until a first purification. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

In another embodiment, methods for preparing a tagged library of target nucleic acid sequences are provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences, and purifying the resulting library. In certain embodiments a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG). apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In particular embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments the purification comprises a single or repeated separating step that is carried out following production of the library following the second amplification; and wherein steps the other method steps are conducted in a single reaction vessel without requisite transferring of a portion (aliquot) of any of the products generated in steps to another reaction vessel. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and the cleavable moieties are included flanking either end of the tag sequence.

In some embodiments, adaptor-dimer byproducts resulting from the first amplification of step of the methods are largely removed from the resulting library. In certain embodiments the enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In particular embodiments adaptor dimer byproducts are eliminated.

In some embodiments, the library is prepared in less than 4 hours. In some embodiments, the library is prepared, enriched and sequenced in less than 3 hours. In some embodiments, the library is prepared, enriched and sequenced in 2 to 3 hours. In some embodiments, the library is prepared in approximately 2.5 hours. In some embodiments, the library is prepared in approximately 2.75 hours. In some embodiments, the library is prepared in approximately 3 hours.

Compositions

Additional aspects of the invention comprise composition comprising a plurality of nucleic acid adaptors, as well as library compositions prepared according to the methods of the invention. Provided compositions are useful in conjunction with the methods described herein as well as for additional analysis and applications known in the art.

Thus, provided are composition comprising a plurality of nucleic acid adaptors, wherein each of the plurality of adaptors comprises a 5′ universal handle sequence, optionally one or more tag sequences, and a 3′ target nucleic acid sequence wherein each adaptor comprises a cleavable moiety, wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, and when tag sequences are present cleavable moieties are included flanking either end of the tag sequence and wherein the universal handle sequence does not include the cleavable moiety. At least two and up to one hundred thousand target specific adaptor pairs are included in provided compositions. Provided composition allow for rapid production of highly multiplexed targeted libraries.

In some embodiments, provided compositions comprise plurality of nucleic acid adaptors, wherein each of the plurality of adaptors comprise a 5′ universal handle sequence, one or more tag sequences, and a 3′ target nucleic acid sequence wherein each adaptor comprises a cleavable moiety; wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety. At least two and up to one hundred thousand target specific adaptor pairs are included in provided compositions. Provided composition allow for rapid production of highly multiplexed, tagged, targeted libraries.

Primer/adaptor compositions may be single stranded or double stranded. In some embodiments adaptor compositions comprise are single stranded adaptors. In some embodiments adaptor compositions comprise double stranded adaptors. In some embodiments adaptor compositions comprise a mixture of single stranded and double stranded adaptors.

In some embodiments, compositions include a plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprising a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences wherein the target-specific primer sequence is substantially non-complementary to other target specific primer sequences in the composition. In some embodiments, the composition comprises at least 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 750, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4500, 5000, 5500, 6000, 7000, 8000, 9000, 10000, 11000, or 12000, or more target-specific adaptor pairs. In some embodiments, target-specific adpator pairs comprise about 15 nucleotides to about 40 nucleotides in length, wherein at least one nucleotide is replaced with a cleavable group. In some embodiments the cleavable group is a uridine nucleotide. In some embodiments, the target-specific adaptor pairs are designed to amplify an exon, gene, exome or region of the genome associated with a clinical or pathological condition, e.g., amplification of one or more sites comprising one or more mutations (e.g., driver mutation) associated with a cancer, e.g., lung, colon, breast cancer, etc., or amplification of mutations associated with an inherited disease, e.g., cystic fibrosis, muscular dystrophies, etc. In some embodiments, the target-specific adaptor pairs when hybridized to a target sequence and amplified as provided herein generates a library of adaptor-ligated amplified target sequences that are about 100 to about 600 base pairs in length. In some embodiments, no one adaptor-ligated amplified target sequence is overexpressed in the library by more than 30% as compared to the remainder of other adaptor-ligated amplified target sequences in the library. In some embodiments, an adaptor-ligated amplified target sequence library is substantially homogenous with respect to GC content, amplified target sequence length or melting temperature (Tm) of the respective target sequences.

In some embodiments, the target-specific primer sequences of adaptor pairs in the compositions of the invention are target-specific sequences that can amplify specific regions of a nucleic acid molecule. In some embodiments, the target-specific adaptors can amplify genomic DNA or cDNA. In some embodiments, target-specific adaptors can amplify mammalian nucleic acid, such as, but not limited to human DNA or RNA, murine DNA or RNA, bovine DNA or RNA, canine DNA or RNA, equine DNA or RNA, or any other mammal of interest. In other embodiments, target specific adaptors include sequences directed to amplify plant nucleic acids of interest. In other embodiments, target specific adaptors include sequences directed to amplify infectious agents, e.g., bacterial and/or viral nucleic acids. In some embodiments, the amount of nucleic acid required for selective amplification is from about 1 ng to 1 microgram. In some embodiments, the amount of nucleic acid required for selective amplification of one or more target sequences is about 1 ng, about 5 ng or about 10 ng. In some embodiments, the amount of nucleic acid required for selective amplification of target sequence is about 10 ng to about 200 ng.

As described herein, each of the plurality of adaptors comprises a 5′ universal handle sequence. In some embodiments a universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In some embodiments the comparable maximal minimum melting temperatures of each adaptor universal handle sequence is higher than the comparable maximal minimum melting temperatures of each target nucleic acid sequence and each tag sequence present in the same adaptor. Preferably, the universal handle sequences of provided adaptors do not exhibit significant complementarity and/or hybridization to any portion of a unique tag sequence and/or target nucleic acid sequence of interest. In some embodiments a first universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In some embodiments a second universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In certain embodiments first and second universal handle sequences correspond to forward and reverse universal handle sequences and in certain embodiments the same first and second universal handle sequences are included for each of the plurality of target specific adaptor pairs. Such forward and reverse universal handle sequences are targeted in conjunction with universal primers to carry out a second amplification of repaired amplicons in production of libraries according to methods of the invention. In certain embodiments a first 5′ universal handle sequence comprises two universal handle sequences (e.g., a combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence); and a second 5′ universal sequence comprises two universal handle sequences (e.g., a combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence), wherein the 5′ first and second universal handle sequences do not exhibit significant hybridization to any portion of a target nucleic acid sequence of interest.

The structure and properties of universal amplification primers or universal primers are well known to those skilled in the art and can be implemented for utilization in conjunction with provided methods and compositions to adapt to specific analysis platforms. Universal handle sequences of the adaptors provided herein are adapted accordingly to accommodate a preferred universal primer sequences. For example, e.g., as described herein universal P1 and A primers with optional barcode sequences have been described in the art and utilized for sequencing on Ion Torrent sequencing platforms (Ion Xpress™ Adapters, Thermo Fisher Scientific). Similarly, additional and other universal adaptor/primer sequences described and known in the art (e.g., Illumina universal adaptor/primer sequences can be found, e.g., at //supportillumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf; PacBio universal adaptor/primer sequences, can be found, e.g., at //s3.amazonaws.com/files.pacb.com/pdf/Guide_Pacific_Biosciences_Template_Preparation_and_Sequencing.pdf; etc.) can be used in conjunction with the methods and compositions provided herein. Suitable universal primers of appropriate nucleotide sequence for use with adaptors of the invention are readily prepared using standard automated nucleic acid synthesis equipment and reagents in routine use in the art. One single type of universal primer or separate types (or even a mixture) of two different universal primers, for example a pair of universal amplification primers suitable for amplification of repaired amplicons in a second amplification are included for use in the methods of the invention. Universal primers optionally include a different tag (barcode) sequence, where the tag (barcode) sequence does not hybridize to the adaptor. Barcode sequences incorporated into amplicons in a second universal amplification can be utilized e.g., for effective identification of sample source.

In some embodiments adaptors further comprise a unique tag sequence located between the 5′ first universal handle sequence and the 3′ target-specific sequence, and wherein the unique tag sequence does not exhibit significant complementarity and/or hybridization to any portion of a unique tag sequence and/or target nucleic acid sequence of interest. In some embodiments the plurality of primer adaptor pairs has 10⁴-10⁹ different tag sequence combinations. Thus in certain embodiments each generated target specific adaptor pair comprises 10⁴-10⁹ different tag sequences. In some embodiments the plurality of primer adaptors comprise each target specific adaptor comprising at least 1 different unique tag sequence and up to 10⁵ different unique tag sequences. In some embodiments the plurality of primer adaptors comprise each target specific adaptor comprising at least 1 different unique tag sequence and up to 10⁵ different unique tag sequences. In certain embodiments each generated target specific amplicon generated comprises at least two and up to 10⁹ different adaptor combinations comprising different tag sequences, each having two different unique tag sequences. In some embodiments the plurality of primer adaptors comprise each target specific adaptor comprising 4096 different tag sequences. In certain embodiments each generated target specific amplicon generated comprises up to 16,777,216 different adaptor combinations comprising different tag sequences, each having two different unique tag sequences.

In some embodiments individual primer adaptors in the plurality of adaptors include a unique tag sequence (e.g., contained in a tag adaptor) comprising different random tag sequences alternating with fixed tag sequences. In some embodiments, the at least one unique tag sequence comprises a at least one random sequence and at least one fixed sequence, or comprises a random sequence flanked on both sides by a fixed sequence, or comprises a fixed sequence flanked on both sides by a random sequence. In some embodiments a unique tag sequence includes a fixed sequence that is 2-2000 nucleotides or base-pairs in length. In some embodiments a unique tag sequence includes a random sequence that is 2-2000 nucleotides or base-pairs in length.

In some embodiments, unique tag sequences include a sequence having at least one random sequence interspersed with fixed sequences. In some embodiments, individual tag sequences in a plurality of unique tags have the structure (N)_(n)(X)_(x)(M)_(m)(Y)_(y), wherein “N” represents a random tag sequence that is generated from A, G, C, T, U or I, and wherein “n” is 2-10 which represents the nucleotide length of the “N” random tag sequence; wherein “X” represents a fixed tag sequence, and wherein “x” is 2-10 which represents the nucleotide length of the “X” random tag sequence; wherein “M” represents a random tag sequence that is generated from A, G, C, T, U or I, wherein the random tag sequence “M” differs or is the same as the random tag sequence “N”, and wherein “m” is 2-10 which represents the nucleotide length of the “M” random tag sequence; and wherein “Y” represents a fixed tag sequence, wherein the fixed tag sequence of “Y” is the same or differs from the fixed tag sequence of “X”, and wherein “y” is 2-10 which represents the nucleotide length of the “Y” random tag sequence. In some embodiments, the fixed tag sequence “X” is the same in a plurality of tags. In some embodiments, the fixed tag sequence “X” is different in a plurality of tags. In some embodiments, the fixed tag sequence “Y” is the same in a plurality of tags. In some embodiments, the fixed tag sequence “Y” is different in a plurality of tags. In some embodiments, the fixed tag sequences “(X)_(x)” and “(Y)_(y)” within the plurality of adaptors are sequence alignment anchors.

In some embodiments, the random sequence within a unique tag sequence is represented by “N”, and the fixed sequence is represented by “X”. Thus, a unique tag sequence is represented by N₁N₂N₃X₁X₂X₃ or by N₁N₂N₃X₁X₂X₃N₄N₅N₆X₄X₅X₆. Optionally, a unique tag sequence can have a random sequence in which some or all of the nucleotide positions are randomly selected from a group consisting of A, G, C, T, U and I. For example, a nucleotide for each position within a random sequence is independently selected from any one of A, G, C, T, U or I, or is selected from a subset of these six different types of nucleotides. Optionally, a nucleotide for each position within a random sequence is independently selected from any one of A, G, C or T. In some embodiments, the first fixed tag sequence “X₁X₂X₃” is the same or different sequence in a plurality of tags. In some embodiments, the second fixed tag sequence “X₄X₅X₆” is the same or different sequence in a plurality of tags. In some embodiments, the first fixed tag sequence “X₁X₂X₃” and the second fixed tag sequence “X₄X₅X₆” within the plurality of adaptors are sequence alignment anchors.

In some embodiments, a unique tag sequence comprises the sequence 5′-NNNACTNNNTGA-3′, where “N” represents a position within the random sequence that is generated randomly from A, G, C or T, the number of possible distinct random tags is calculated to be 4⁶ (or 4{circumflex over ( )}6) is about 4096, and the number of possible different combinations of two unique tags is 4¹² (or 4{circumflex over ( )}12) is about 16.78 million. In some embodiments, the underlined portions of 5′-NNNACTNNNTGA-3′ are a sequence alignment anchor.

In some embodiments, the fixed sequences within the unique tag sequence is a sequence alignment anchor that can be used to generate error-corrected sequencing data. In some embodiments fixed sequences within the unique tag sequence is a sequence alignment anchor that can be used to generate a family of error-corrected sequencing reads.

Adaptors provided herein comprise at least one cleavable moiety. In some embodiments a cleavable moiety is within the 3′ target-specific sequence. In some embodiments a cleavable moiety is at or near the junction between the 5′ first universal handle sequence and the 3′ target-specific sequence. In some embodiments a cleavable moiety is at or near the junction between the 5′ first universal handle sequence and the unique tag sequence, and at or near the junction between the unique tag sequence and the 3′ target-specific sequence. The cleavable moiety can be present in a modified nucleotide, nucleoside or nucleobase. In some embodiments, the cleavable moiety can include a nucleobase not naturally occurring in the target sequence of interest.

In some embodiments the at least one cleavable moiety in the plurality of adaptors is a uracil base, uridine or a deoxyuridine nucleotide. In some embodiments a cleavable moiety is within the 3′ target-specific sequence and the junctions between the 5′ universal handle sequence and the unique tag sequence and/or the 3′target specific sequence wherein the at least one cleavable moiety in the plurality of adaptors is cleavable with uracil DNA glycosylase (UDG). In some embodiments, a cleavable moiety is cleaved, resulting in a susceptible abasic site, wherein at least one enzyme capable of reacting on the abasic site generates a gap comprising an extendible 3′ end. In certain embodiments the resulting gap comprises a 5′-deoxyribose phosphate group. In certain embodiments the resulting gap comprises an extendible 3′ end and a 5′ ligatable phosphate group.

In another embodiment, inosine can be incorporated into a DNA-based nucleic acid as a cleavable group. In one exemplary embodiment, EndoV can be used to cleave near the inosine residue. In another exemplary embodiment, the enzyme hAAG can be used to cleave inosine residues from a nucleic acid creating abasic sites.

Where a cleavable moiety is present, the location of the at least one cleavable moiety in the adaptors does not significantly change the melting temperature (Tm) of any given double-stranded adaptor in the plurality of double-stranded adaptors. The melting temperatures (Tm) of any two given double-stranded adaptors from the plurality of double-stranded adaptors are substantially the same, wherein the melting temperatures (Tm) of any two given double-stranded adaptors does not differ by more than 10° C. of each other. However, within each of the plurality of adaptors, the melting temperatures of sequence regions differs, such that the comparable maximal minimum melting temperature of, for example, the universal handle sequence, is higher than the comparable maximal minimum melting temperatures of either the unique tag sequence and/or the target specific sequence of any adaptor. This localized differential in comparable maximal minimum melting temperatures can be adjusted to optimize digestion and repair of amplicons and ultimately improved effectiveness of the methods provided herein.

Further provided are compositions comprising a nucleic acid library generated by methods of the invention. Thus, provided are composition comprising a plurality of amplified target nucleic acid amplicons, wherein each of the plurality of amplicons comprises a 5′ universal handle sequence, optionally a first unique tag sequences, an intermediate target nucleic acid sequence, optionally a second unique tag sequences and a 3′ universal handle sequence. At least two and up to one hundred thousand target specific amplicons are included in provided compositions. Provided compositions include highly multiplexed targeted libraries. In some embodiments, provided compositions comprise a plurality of nucleic acid amplicons, wherein each of the plurality of amplicons comprise a 5′ universal handle sequence, a first unique tag sequences, an intermediate target nucleic acid sequence, a second unique tag sequences and a 3′ universal handle sequence. At least two and up to one hundred thousand target specific tagged amplicons are included in provided compositions. Provided compositions include highly multiplexed tagged targeted libraries.

In some embodiments, library compositions include a plurality of target specific amplicons comprising a multiplex of at least two different target nucleic acid sequences. In some embodiments, the composition comprises at least 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 750, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4500, 5000, 5500, 6000, 7000, 8000, 9000, 10000, 11000, or 12000, or more target-specific amplicons. In some embodiments, the target-specific amplicons comprise one or more exon, gene, exome or region of the genome associated with a clinical or pathological condition, e.g., amplicons comprising one or more sites comprising one or more mutations (e.g., driver mutation) associated with a cancer, e.g., lung, colon, breast cancer, etc., or amplicons comprising mutations associated with an inherited disease, e.g., cystic fibrosis, muscular dystrophies, etc. In some embodiments, the target-specific amplicons comprise a library of adaptor-ligated amplicon target sequences that are about 100 to about 750 base pairs in length.

As described herein, each of the plurality of amplicons comprises a 5′ universal handle sequence. In some embodiments a universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. Preferably, the universal handle sequences of provided adaptors do not exhibit significant complementarity and/or hybridization to any portion of a unique tag sequence and/or target nucleic acid sequence of interest. In some embodiments a first universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In some embodiments a second universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In certain embodiments first and second universal handle sequences correspond to forward and reverse universal handle sequences and in certain embodiments the same first and second universal handle sequences are included for each of the plurality of target specific amplicons. Such forward and reverse universal handle sequences are targeted in conjunction with universal primers to carry out a second amplification of a preliminary library composition in production of resulting amplified according to methods of the invention. In certain embodiments a first 5′ universal handle sequence comprises two universal handle sequences (e.g., a combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence); and a second 5′ universal sequence comprises two universal handle sequences (e.g., a combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence), wherein the 5′ first and second universal handle sequences do not exhibit significant hybridization to any portion of a target nucleic acid sequence of interest.

The structure and properties of universal amplification primers or universal primers are well known to those skilled in the art and can be implemented for utilization in conjunction with provided methods and compositions to adapt to specific analysis platforms. Universal handle sequences of the adaptors and amplicons provided herein are adapted accordingly to accommodate a preferred universal primer sequences. For example, e.g., as described herein universal P1 and A primers with optional barcode sequences have been described in the art and utilized for sequencing on Ion Torrent sequencing platforms (Ion Xpress™ Adapters, Thermo Fisher Scientific). Similarly, additional and other universal adaptor/primer sequences described and known in the art (e.g., Illumina universal adaptor/primer sequences can be found, e.g., at //support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf; PacBio universal adaptor/primer sequences, can be found, e.g., at //s3.amazonaws.com/files.pacb.com/pdf/Guide_Pacific_Biosciences_Template_Preparation_and_Sequencing.pdf; etc.) can be used in conjunction with the methods and compositions provided herein. Suitable universal primers of appropriate nucleotide sequence for use with libraries of the invention are readily prepared using standard automated nucleic acid synthesis equipment and reagents in routine use in the art. One single type or separate types (or even a mixture) of two different universal primers, for example a pair of universal amplification primers suitable for amplification of a preliminary library may be used in production of the libraries of the invention. Universal primers optionally include a tag (barcode) sequence, where the tag (barcode) sequence does not hybridize to adaptor sequence or to target nucleic acid sequences. Barcode sequences incorporated into amplicons in a second universal amplification can be utilized e.g., for effective identification of sample source to thereby generate a barcoded library. Thus provided compositions include highly multiplexed barcoded targeted libraries. Provided compositions also include highly multiplexed barcoded tagged targeted libraries.

In some embodiments amplicon libraries comprise a unique tag sequence located between the 5′ first universal handle sequence and the 3′ target-specific sequence, and wherein the unique tag sequence does not exhibit significant complementarity and/or hybridization to any portion of a unique tag sequence and/or target nucleic acid sequence. In some embodiments the plurality of amplicons has 10⁴-10⁹ different tag sequence combinations. Thus in certain embodiments each of the plurality of amplicons in a library comprises 10⁴-10⁹ different tag sequences. In some embodiments each of the plurality of amplicons in a library comprises at least 1 different unique tag sequence and up to 10⁵ different unique tag sequences. In certain embodiments each target specific amplicon in a library comprises at least two and up to 10⁹ different combinations comprising different tag sequences, each having two different unique tag sequences. In some embodiments each of the plurality of amplicons in a library comprise a tag sequence comprising 4096 different tag sequences. In certain embodiments each target specific amplicon of a library comprises up to 16,777,216 different combinations comprising different tag sequences, each having two different unique tag sequences.

In some embodiments individual amplicons in the plurality of amplicons of a library include a unique tag sequence (e.g., contained in a tag adaptor sequence) comprising different random tag sequences alternating with fixed tag sequences. In some embodiments, the at least one unique tag sequence comprises a at least one random sequence and at least one fixed sequence, or comprises a random sequence flanked on both sides by a fixed sequence, or comprises a fixed sequence flanked on both sides by a random sequence. In some embodiments a unique tag sequence includes a fixed sequence that is 2-2000 nucleotides or base-pairs in length. In some embodiments a unique tag sequence includes a random sequence that is 2-2000 nucleotides or base-pairs in length.

In some embodiments, unique tag sequences include a sequence having at least one random sequence interspersed with fixed sequences. In some embodiments, individual tag sequences in a plurality of unique tags have the structure (N)_(n)(X)_(x)(M)_(m)(Y)_(y), wherein “N” represents a random tag sequence that is generated from A, G, C, T, U or I, and wherein “n” is 2-10 which represents the nucleotide length of the “N” random tag sequence; wherein “X” represents a fixed tag sequence, and wherein “x” is 2-10 which represents the nucleotide length of the “X” random tag sequence; wherein “M” represents a random tag sequence that is generated from A, G, C, T, U or I, wherein the random tag sequence “M” differs or is the same as the random tag sequence “N”, and wherein “m” is 2-10 which represents the nucleotide length of the “M” random tag sequence; and wherein “Y” represents a fixed tag sequence, wherein the fixed tag sequence of “Y” is the same or differs from the fixed tag sequence of “X”, and wherein “y” is 2-10 which represents the nucleotide length of the “Y” random tag sequence. In some embodiments, the fixed tag sequence “X” is the same in a plurality of tags. In some embodiments, the fixed tag sequence “X” is different in a plurality of tags. In some embodiments, the fixed tag sequence “Y” is the same in a plurality of tags. In some embodiments, the fixed tag sequence “Y” is different in a plurality of tags. In some embodiments, the fixed tag sequences “(X)_(x)” and “(Y)_(y)” within the plurality of amplicons are sequence alignment anchors.

In some embodiments, the random sequence within a unique tag sequence is represented by “N”, and the fixed sequence is represented by “X”. Thus, a unique tag sequence is represented by N₁N₂N₃X₁X₂X₃ or by N₁N₂N₃X₁X₂X₃N₄N₅N₆X₄X₅X₆. Optionally, a unique tag sequence can have a random sequence in which some or all of the nucleotide positions are randomly selected from a group consisting of A, G, C, T, U and I. For example, a nucleotide for each position within a random sequence is independently selected from any one of A, G, C, T, U or I, or is selected from a subset of these six different types of nucleotides. Optionally, a nucleotide for each position within a random sequence is independently selected from any one of A, G, C or T. In some embodiments, the first fixed tag sequence “X₁X₂X₃” is the same or different sequence in a plurality of tags. In some embodiments, the second fixed tag sequence “X₄X₅X₆” is the same or different sequence in a plurality of tags. In some embodiments, the first fixed tag sequence “X₁X₂X₃” and the second fixed tag sequence “X₄X₅X₆” within the plurality of amplicons are sequence alignment anchors.

In some embodiments, a unique tag sequence comprises the sequence 5′-NNNACTNNNTGA-3′, where “N” represents a position within the random sequence that is generated randomly from A, G, C or T, the number of possible distinct random tags is calculated to be 4⁶ (or 4{circumflex over ( )}6) is about 4096, and the number of possible different combinations of two unique tags is 4¹² (or 4{circumflex over ( )}12) is about 16.78 million. In some embodiments, the underlined portions of 5′-NNNACTNNNTGA-3′ are a sequence alignment anchor.

In some embodiments, the fixed sequences within the unique tag sequence is a sequence alignment anchor that can be used to generate error-corrected sequencing data. In some embodiments fixed sequences within the unique tag sequence is a sequence alignment anchor that can be used to generate a family of error-corrected sequencing reads.

Kits, Systems

Further provided herein are kits for use in preparing libraries of target nucleic acids using methods of the first or second aspects of the invention. Embodiments of a kit comprise a supply of at least a pair of target specific adaptors as defined herein which are capable of producing a first amplification product; as well as optionally a supply of at least one universal pair of amplification primers capable of annealing to the universal handle(s) of the adaptor and priming synthesis of an amplification product, which amplification product would include a target sequence of interest ligated to a universal sequence. Adaptors and/or primers may be supplied in kits ready for use, or more preferably as concentrates requiring dilution before use, or even in a lyophilized or dried form requiring reconstitution prior to use. In certain embodiments kits further include a supply of a suitable diluent for dilution or reconstitution of the components. Optionally, kits further comprise supplies of reagents, buffers, enzymes, dNTPs, etc., for use in carrying out amplification, digestion, repair, and/or purification in the generation of library as provided herein. Non-limiting examples of such reagents are as described in the Materials and Methods sections of the accompanying Exemplification. Further components which optionally are supplied in the kit include components suitable for purification of libraries prepared using the provided methods. In some embodiments, provided is a kit for generating a target-specific library comprising a plurality of target-specific adaptors having a 5′ universal handle sequence, a 3′ target specific sequence and a cleavable group, a DNA polymerase, an adaptor, dATP, dCTP, dGTP, dTTP, and a digestion reagent. In some embodiments, the kit further comprises one or more antibodies, a repair reagent, universal primers optionally comprising nucleic acid barcodes, purification solutions or columns.

Particular features of adaptors for inclusion in kits are as described elsewhere herein in relation to other aspects of the invention. The structure and properties of universal amplification primers are well known to those skilled in the art and can be implemented for utilization in conjunction with provided methods and compositions to adapt to specific analysis platforms (e.g., as described herein universal P1 and A primers have been described in the art and utilized for sequencing on Ion Torrent sequencing platforms). Similarly, additional and other universal adaptor/primer sequences described and known in the art (e.g., Illumina universal adaptor/primer sequences, PacBio universal adaptor/primer sequences, etc.) can be used in conjunction with the methods and compositions provided herein. Suitable primers of appropriate nucleotide sequence for use with adaptors included in the kit is readily prepared using standard automated nucleic acid synthesis equipment and reagents in routine use in the art. A kit may include a supply of one single type of universal primer or separate types (or even a mixture) of two different universal primers, for example a pair of amplification primers suitable for amplification of templates modified with adaptors in a first amplification. A kit may comprise at least a pair of adaptors for first amplification of a sample of interest according to the methods of the invention, plus at least two different amplification primers that optionally carry a different tag (barcode) sequence, where the tag (barcode) sequence does not hybridize to the adaptor. A kit can be used to amplify at least two different samples where each sample is amplified according to methods of the invention separately and a second amplification comprises using a single universal primer having a barcode, and then pooling prepared sample libraries after library preparations. In some embodiments a kit includes different universal primer-pairs for use in second amplification step described herein. In this context the ‘universal’ primer-pairs may be of substantially identical nucleotide sequence but differ with respect to some other feature or modification.

Further provided are systems, e.g., systems used to practice methods provided herein, and/or comprising compositions provided herein. In some embodiments, systems facilitate methods carried out in automated mode. In certain embodiments, systems facilitate high throughput mode. In certain embodiments, systems include, e.g., a fluid handling element, a fluid containing element, a heat source and/or heat sink for achieving and maintaining a desired reaction temperature, and/or a robotic element capable of moving components of the system from place to place as needed (e.g., a multiwell plate handling element).

Samples

As defined herein, “sample” and its derivatives, is used in its broadest sense and includes any specimen, culture and/or the like that is suspected of including a target nucleic acid. In some embodiments, a sample comprises DNA, RNA, chimeric nucleic acid, hybrid nucleic acid, multiplex-forms of nucleic acids or any combination of two or more of the foregoing. In some embodiments a sample useful in conjunction with methods of the invention includes any biological, clinical, surgical, agricultural, atmospheric or aquatic-based specimen containing one or more target nucleic acid of interest. In some embodiments, a sample includes nucleic acid molecules obtained from an animal such as a human or mammalian source. In another embodiment, a sample includes nucleic acid molecules obtained from a non-mammalian source such as a plant, bacteria, virus or fungus. In some embodiments, the source of the nucleic acid molecules may be an archived or extinct sample or species. In some embodiments a sample includes isolated nucleic acid sample prepared, for example, from a source such as genomic DNA, RNA or a prepared sample such as, e.g., fresh-frozen or formalin-fixed paraffin-embedded (FFPE) nucleic acid specimen. It is also envisioned that a sample is from a single individual, a collection of nucleic acid samples from genetically related members, multiple nucleic acid samples from genetically unrelated members, multiple nucleic acid samples (matched) from a single individual such as a tumor sample and normal tissue sample, or genetic material from a single source that contains two distinct forms of genetic material such as maternal and fetal DNA obtained from a maternal subject, or the presence of contaminating bacteria DNA in a sample that contains plant or animal DNA. In some embodiments, a source of nucleic acid material includes nucleic acids obtained from a newborn (e.g., a blood sample for newborn screening). In some embodiments, provided methods comprise amplification of multiple target-specific sequences from a single nucleic acid sample. In some embodiments, provided methods comprise target-specific amplification of two or more target sequences from two or more nucleic acid samples or species. In certain embodiments, provided methods comprise amplification of highly multiplexed target nucleic acid sequences from a single sample. In particular embodiments, provided methods comprise amplification of highly multiplexed target nucleic acid sequences from more than one sample, each from the same source organism.

In some embodiments a sample comprises a mixture of target nucleic acids and non-target nucleic acids. In certain embodiments a sample comprises a plurality of initial polynucleotides which comprises a mixture of one or more target nucleic acids and may include one or more non-target nucleic acids. In some embodiments a sample comprising a plurality of polynucleotides comprises a portion or aliquot of an originating sample; in some embodiments, a sample comprises a plurality of polynucleotides which is the entire originating sample. In some embodiments a sample comprises a plurality of initial polynucleotides is isolated from the same source or from the same subject at different time points.

In some embodiments, a nucleic acid sample includes cell-free nucleic acids from a biological fluid, nucleic acids from a tissue, nucleic acids from a biopsied tissue, nucleic acids from a needle biopsy, nucleic acids from a single cell or nucleic acids from two or more cells. In certain embodiments, a single reaction mixture contains 1-100 ng of the plurality of initial polynucleotides. In some embodiments a plurality of initial polynucleotides comprises a formalin fixed paraffin-embedded (FFPE) sample; genomic DNA; RNA; cell free DNA or RNA; circulating tumor DNA or RNA; fresh frozen sample, or a mixture of two or more of the foregoing; and in some embodiments a the plurality of initial polynucleotides comprises a nucleic acid reference standard. In some embodiments, a sample includes nucleic acid molecules obtained from biopsies, tumors, scrapings, swabs, blood, mucus, urine, plasma, semen, hair, laser capture micro-dissections, surgical resections, and other clinical or laboratory obtained sample. In some embodiments, a sample is an epidemiological, agricultural, forensic or pathogenic sample. In certain embodiments, a sample includes a reference. In some embodiments a sample is a normal tissue or well documented tumor sample. In certain embodiments a reference is a standard nucleic acid sequence (e.g., Hg19).

Target Nucleic Acid Sequence Analysis

Provided methods and compositions of the invention are particularly suitable for amplifying, optionally tagging, and preparing target sequences for subsequent analysis. Thus, in some embodiments, methods provided herein include analyzing resulting library preparations. For example, methods comprise analysis of a polynucleotide sequence of a target nucleic acid, and, where applicable, analysis of any tag sequence(s) added to a target nucleic acid. In some embodiments wherein multiple target nucleic acid regions are amplified, provided methods include determining polynucleotide sequences of multiple target nucleic acids. Provided methods further optionally include using a second tag sequence(s), e.g., barcode sequence, to identify the source of the target sequence (or to provide other information about the sample source). In certain embodiments, use of prepared library composition is provided for analysis of the sequences of the nucleic acid library.

In particular embodiments, use of prepared tagged library compositions is provided for further analyzing the sequences of the target nucleic acid library. In some embodiments determination of sequences comprises determining the abundance of at least one of the target sequences in the sample. In some embodiments determination of a low frequency allele in a sample is comprised in determination of sequences of a nucleic acid library. In certain embodiments, determination of the presence of a mutant target nucleic acid in the plurality of polynucleotides is comprised in determination of sequences of a nucleic acid library. In some embodiments, determination of the presence of a mutant target nucleic acid comprises detecting the abundance level of at least one mutant target nucleic acid in the plurality of polynucleotides. For example, such determination comprises detecting at least one mutant target nucleic acid is present at 0.05% to 1% of the original plurality of polynucleotides in the sample, detecting at least one mutant target nucleic acid is present at about 1% to about 5% of the polynucleotides in the sample, and/or detecting at least 85%-100% of target nucleic acids in sample. In some embodiments, determination of the presence of a mutant target nucleic acid comprises detecting and identification of copy number variation and/or genetic fusion sequences in a sample.

In some embodiments, nucleic acid sequencing of the amplified target sequences produced by the teachings of this disclosure include de novo sequencing or targeted re-sequencing. In some embodiments, nucleic acid sequencing further includes comparing the nucleic acid sequencing results of the amplified target sequences against a reference nucleic acid sequence. In some embodiments, nucleic acid sequencing of the target library sequences further includes determining the presence or absence of a mutation within a nucleic acid sequence. In some embodiments, nucleic acid sequencing includes the identification of genetic markers associated with disease (e.g., cancer and/or inherited disease).

In some embodiments, prepared library of target sequences of the disclosed methods is used in various downstream analysis or assays with, or without, further purification or manipulation. In some embodiments analysis comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In certain embodiments analysis is carried out by high throughput next generation sequencing. In particular embodiments sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon.

In some embodiments, library prepared according to the methods provided herein is then further manipulated for additional analysis. For example, \ prepared library sequences is used in downstream enrichment techniques known in the art, such a bridge amplification or emPCR to generate a template library that is then used in next generation sequencing. In some embodiments, the target nucleic acid library is used in an enrichment application and a sequencing application. For example, sequence determination of a provided target nucleic acid library is accomplished using any suitable DNA sequencing platform. In some embodiments, the library sequences of the disclosed methods or subsequently prepared template libraries is used for single nucleotide polymorphism (SNP) analysis, genotyping or epigenetic analysis, copy number variation analysis, gene expression analysis, analysis of gene mutations including but not limited to detection, prognosis and/or diagnosis, detection and analysis of rare or low frequency allele mutations, nucleic acid sequencing including but not limited to de novo sequencing, targeted resequencing and synthetic assembly analysis. In one embodiment, prepared library sequences are used to detect mutations at less than 5% allele frequency. In some embodiments, the methods disclosed herein is used to detect mutations in a population of nucleic acids at less than 4%, 3%, 2% or at about 1% allele frequency. In another embodiment, libraries prepared as described herein are sequenced to detect and/or identify germline or somatic mutations from a population of nucleic acid molecules. In certain embodiments, sequencing adaptors are ligated to the ends of the prepared libraries generate a plurality of libraries suitable for nucleic acid sequencing.

In some embodiments, methods for preparing a target-specific amplicon library are provided for use in a variety of downstream processes or assays such as nucleic acid sequencing or clonal amplification. In some embodiments, the library is amplified using bridge amplification or emPCR to generate a plurality of clonal templates suitable for nucleic acid sequencing. For example, optionally following target-specific amplification a secondary and/or tertiary amplification process including, but not limited to, a library amplification step and/or a clonal amplification step is performed. “Clonal amplification” refers to the generation of many copies of an individual molecule. Various methods known in the art is used for clonal amplification. For example, emulsion PCR is one method, and involves isolating individual DNA molecules along with primer-coated beads in aqueous bubbles within an oil phase. A polymerase chain reaction (PCR) then coats each bead with clonal copies of the isolated library molecule and these beads are subsequently immobilized for later sequencing. Emulsion PCR is used in the methods published by Marguilis et al. and Shendure and Porreca et al. (also known as “polony sequencing”, commercialized by Agencourt and recently acquired by Applied Biosystems). Margulies, et al. (2005) Nature 437: 376-380; Shendure et al., Science 309 (5741): 1728-1732. Another method for clonal amplification is “bridge PCR,” where fragments are amplified upon primers attached to a solid surface. These methods, as well as other methods of clonal amplification, both produce many physically isolated locations that each contain many copies derived from a single molecule polynucleotide fragment. Thus, in some embodiments, the one or more target specific amplicons are amplified using for example, bridge amplification or emPCR to generate a plurality of clonal templates suitable for nucleic acid sequencing.

In some embodiments, at least one of the library sequences to be clonally amplified are attached to a support or particle. A support can be comprised of any suitable material and have any suitable shape, including, for example, planar, spheroid or particulate. In some embodiments, the support is a scaffolded polymer particle as described in U.S. Published App. No. 20100304982, hereby incorporated by reference in its entirety. In certain embodiments methods comprise depositing at least a portion of an enriched population of library sequences onto a support (e.g., a sequencing support), wherein the support comprises an array of sequencing reaction sites. In some embodiments, an enriched population of library sequences are attached to the sequencing reaction sites on the support. wherein the support comprises an array of 10²-10¹⁰ sequencing reaction sites.

Sequence determination means determination of information relating to the sequence of a nucleic acid and may include identification or determination of partial as well as full sequence information of the nucleic acid. Sequence information may be determined with varying degrees of statistical reliability or confidence. In some embodiments sequence analysis includes high throughput, low depth detection such as by qPCR, rtPCR, and/or array hybridization detection methodologies known in the art. In some embodiments, sequencing analysis includes the determination of the in depth sequence assessment, such as by Sanger sequencing or other high throughput next generation sequencing methods. Next-generation sequencing means sequence determination using methods that determine many (typically thousands to billions) nucleic acid sequences in an intrinsically massively parallel manner, e.g. where many sequences are read out, e.g., in parallel, or alternatively using an ultra-high throughput serial process that itself may be parallelized. Thus, in certain embodiments, methods of the invention include sequencing analysis comprising massively parallel sequencing. Such methods include but are not limited to pyrosequencing (for example, as commercialized by 454 Life Sciences, Inc., Branford, Conn.); sequencing by ligation (for example, as commercialized in the SOLiD™. technology, Life Technologies, Inc., Carlsbad, Calif.); sequencing by synthesis using modified nucleotides (such as commercialized in TruSeq™ and HiSeg™. technology by Illumina, Inc., San Diego, Calif.; HeliScope™ by Helicos Biosciences Corporation, Cambridge, Mass.; and PacBio Sequel® or RS systems by Pacific Biosciences of California, Inc., Menlo Park, Calif.), sequencing by ion detection technologies (e.g., Ion Torrent™ technology, Life Technologies, Carlsbad, Calif.); sequencing of DNA nanoballs (Complete Genomics, Inc., Mountain View, Calif.); nanopore-based sequencing technologies (for example, as developed by Oxford Nanopore Technologies, LTD, Oxford, UK), and like highly parallelized sequencing methods.

For example, in certain embodiments, libraries produced by the teachings of the present disclosure are sufficient in yield to be used in a variety of downstream applications including the Ion Xpress™ Template Kit using an Ion Torrent™ PGM system (e.g., PCR-mediated addition of the nucleic acid fragment library onto Ion Sphere™ Particles)(Life Technologies, Part No. 4467389) or Ion Torrent Proton™ system). For example, instructions to prepare a template library from the amplicon library can be found in the Ion Xpress Template Kit User Guide (Life Technologies, Part No. 4465884), hereby incorporated by reference in its entirety. Instructions for loading the subsequent template library onto the Ion Torrent™ Chip for nucleic acid sequencing are described in the Ion Sequencing User Guide (Part No. 4467391), hereby incorporated by reference in its entirety. Similarly, sequencing using other platforms (e.g., PacBio, Illumina, Helicos, Complete Genomics, Oxford Nanopore) may be carried out using adapted methodologies to incorporate the relevant template preparation according to the instructions and guidance provided with each of the respective platforms.

The initiation point for the sequencing reaction may be provided by annealing a sequencing primer to a product of a solid-phase amplification reaction. In this regard, one or both of the adaptors added during formation of template library may include a nucleotide sequence which permits annealing of a sequencing primer to amplified products derived by whole genome or solid-phase amplification of the template library. Depending on implementation of an embodiment of the invention, a tag sequence and/or target nucleic acid sequence may be determined in a single read from a single sequencing primer, or in multiple reads from two different sequencing primers. In the case of two reads from two sequencing primers, a ‘tag read’ and a ‘target sequence read’ are performed in either order, with a suitable denaturing step to remove an annealed primer after the first sequencing read is completed.

In some embodiments, a sequencer is coupled to server that applies parameters or software to determine the sequence of the amplified target nucleic acid molecules. In certain embodiments, the sequencer is coupled to a server that applies parameters or software to determine the presence of a low frequency mutation allele present in a sample.

EMBODIMENTS

In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. Optionally one or more tag sequences are comprised in each of the plurality of adaptors. Such methods thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG) apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG) formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and a tag sequence is included in at least one adaptor, and the cleavable moieties are included flanking either end of the tag sequence, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. Such methods thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG) apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG) formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety and the melting temperature of each universal sequence is higher than the melting temperature of each target nucleic acid sequence and each tag sequence present. Optionally one or more tag sequences are comprised in each of the plurality of adaptors. Such methods thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG) apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG) formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. Optionally one or more tag sequences are comprised in each of the plurality of adaptors. Such methods are carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG) apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG) formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and all of the adaptors comprise tag sequences having cleavable groups flanking either end of the tag sequence, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. Such methods thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG) apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG) formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

In one embodiment, provided is a method for preparing a library of target nucleic acid sequences comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification, digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons, and amplifying the repaired target amplicons in a second amplification using universal primers; wherein each of the plurality of adaptors comprises a universal handle sequence, one or more tag sequences, a target nucleic acid sequence and a cleavable moiety; and wherein at least two and up to one hundred thousand target specific adaptor pairs are included and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included in the flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety. In certain embodiments the melting temperature of each universal sequence is higher than the melting temperature of each target nucleic acid sequence and each tag sequence present. Such methods thereby produce a library of target nucleic acid sequence. In particular embodiments such methods are carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of two or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of target nucleic acid sequences. In certain embodiments all of the adaptors comprise tag sequences having cleavable groups flanking either end of the tag sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG) apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG) formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

In one embodiment provided is a composition comprising a plurality of nucleic acid adaptors, wherein each of the plurality of adaptors comprise a 5′ universal handle sequence, one or more tag sequences, and a 3′ target nucleic acid sequence wherein each adaptor comprises a cleavable moiety, the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety, and at least two and up to one hundred thousand target specific adaptor pairs are included. In some embodiments the melting temperature of each adaptor universal sequence is higher than the melting temperature of each target nucleic acid sequence and each tag sequence present in the same adaptor. The provided compositions allow for rapid production of highly multiplexed targeted libraries. In particular embodiments, the composition comprises multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In certain embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences In certain embodiments, compositions each generated target specific amplicon produced by target specific pairs of the plurality of adaptors produces at least 1 different sequence and up to 10⁷ different sequences. The foregoing compositions comprise adaptors wherein they are single stranded or double stranded. Yet additional embodiments provide kits comprising the adaptor compositions of any of the foregoing embodiments. In some embodiments such kits further comprise any one or more of an amplification reagent, a digestion reagent and a repair reagent. In certain embodiments such kits further comprise an amplification reagent, a digestion reagent and a repair reagent.

EXEMPLIFICATION Example 1

Provided methods of the invention comprise streamlined procedures enabling rapid, highly multiplexed PCR. See FIG. 1. The invention optionally allows for the incorporation of one or more unique tag sequences, if so desired. Exemplary methods of the invention comprise the following protocols:

Example 1A

Materials and Method

Optional Reverse Transcription (RT) Reaction method (10 uL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

2 uL 5× SuperScript™ VILO™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤8 uL volume of DNA+RNA sample for ≤20 ng total amount of DNA+RNA sample (˜1% RNA sample of the total nucleic acid (TNA));

nuclease-free H2O to the above tube/well to make 10 uL total reaction volume;

Method:

42 C for 30 min

85 C for 1 min

4 C hold (indefinitely)

Amplification:

Materials

ul dH₂O (to 30 ul final) ul 20 ng genomic DNA sample  48 nM Panel of Adaptors  15 ul PhusionU multiplex PCR master mix 2.4 ul 2 u/ul Phusion U DNA polymerase

Amplification:

-   -   98 C for 2 min     -   3 cycles of the following:         -   98 C for 30 s         -   64 C for 2 min         -   62 C for 2 min         -   60 C for 4 min         -   58 C for 2 min         -   72 C for 30 s     -   72 C for 2 min     -   4 C hold (indefinitely).

Digestion, Fill-in, Ligation:

Materials

  2 ul (5 u/ul) UDG,   4 ul (10 u/ul) FPG 0.5 ul (10 u/ul) T4 PNK   1 ul (3000 u/ul) T7 ligase   1 ul (10 mM) ATP.

Method

Mix the materials above, add to reaction mixture.

Incubate:

-   -   30 C for 20 min     -   55 C for 20 min     -   25 C for 10 min     -   98 C for 2 min     -   4 C hold (indefinitely)

The resulting repaired sample is purified using 35 ul Ampure® beads (Beckman Coulter, Inc.) according to the manufacturer instructions.

Amplification:

Materials

1 ul for each P1 and A-universal primers, optionally containing barcode sequence (Ion

Xpress™ Adapters, Thermo Fisher Scientific)

Method

Incubate:

-   -   98 C for 2 min

22 cycles of

-   -   98 C for 15 s     -   64 C for 15 s     -   72 C for 15 s

72 C for 5 min

4 C hold (indefinitely)

The resulting sample is purified using 35 ul Ampure® beads (Beckman Coulter, Inc.) according to the manufacturer instructions. Optionally, the purification step is repeated 1× to 2×.

Example 1B

Materials and Method

Optional Reverse Transcription (RT) Reaction method (10 uL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

2 uL 5× SuperScript™ VILO™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤8 uL volume of DNA+RNA sample for ≤20 ng total amount of DNA+RNA sample (˜1% RNA sample of the total nucleic acid (TNA));

nuclease-free H2O to the above tube/well to make 10 uL total reaction volume;

Method:

42 C for 30 min

85 C for 1 min

4 C hold (indefinitely)

Amplification:

Materials

ul dH₂O (to 30 ul final) ul 20 ng genomic DNA sample  48 nM Panel of Adaptors  15 ul PhusionU multiplex PCR master mix 2.4 ul 2 u/ul Phusion U DNA polymerase

Amplification:

-   -   98 C for 2 min     -   3 cycles of the following:         -   98 C for 30 s         -   64 C for 2 min         -   62 C for 2 min         -   60 C for 4 min         -   58 C for 2 min         -   72 C for 30 s     -   72 C for 2 min     -   4 C hold (indefinitely).

Digestion, Fill-in, Ligation:

Materials

  2 ul (5 u/ul) UDG,   4 ul (10 u/ul) APE1 0.5 ul (1 u/ul) Taq polymerase   1 ul (3000 u/ul) T7 ligase   1 ul (10 mM) ATP.

Method

Mix the materials above, add to reaction mixture.

Incubate:

-   -   30 C for 20 min     -   55 C for 20 min     -   25 C for 10 min     -   98 C for 2 min     -   4 C hold (indefinitely)

Amplification:

Materials

-   -   1 ul for each P1 and A-universal primers, optionally containing         barcode sequence (Ion Xpress™ Adapters, Thermo Fisher         Scientific)

Method

Incubate:

-   -   98 C for 2 min

22 cycles of

-   -   98 C for 15 s     -   64 C for 15 s     -   72 C for 15 s

72 C for 5 min

4 C hold (indefinitely)

The resulting sample is purified using 35 ul Ampure® beads (Beckman Coulter, Inc.) according to the manufacturer instructions. Optionally, purification step may be repeated 1× to 2×.

Example 1C

Materials and Method

Optional Reverse Transcription (RT) Reaction method (10 uL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

2 uL 5× SuperScript™ VILO™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤8 uL volume of DNA+RNA sample for ≤20 ng total amount of DNA+RNA sample (˜1% RNA sample of the total nucleic acid (TNA));

nuclease-free H2O to the above tube/well to make 10 uL total reaction volume;

Method:

42 C for 30 min

85 C for 1 min

4 C hold (indefinitely)

Amplification:

Materials

_ul dH₂O (to 30 ul final) _ul Genomic DNA sample (~20 ng)   6 ul Adaptor Panel 250 nM  15 ul PhusionU multiplex PCR master mix (F-562) 3.0 ul 2 u/ul SuperFiU DNA Polymerase

Amplification

-   -   Assemble mixture of materials in reaction in 96-well plate         wells, amplify using method:     -   99 C for 2 min     -   3 cycles of the following:         -   99 C for 30 s         -   64 C for 2 min         -   62 C for 2 min         -   60 C for 4 min         -   58 C for 2 min         -   72 C for 30 s     -   72 C for 2 min     -   4 C hold (indefinitely)

Digestion, Fill-in, Ligation:

Materials

0.1 ul VIP Oligo 10 uM (P/N 4385451 Thermo Fisher Scientific, Inc.) 2 ul (5 u/ul) UDG 4 ul (10 u/ul) APE1 (NEB, M0282L) 0.5 ul (1 u/ul) Taq polymerase (EP0404) 1 ul (3000 u/ul) T7 ligase (NEB M0318L) 1 ul (10 mM) ATP

Method

Mix the above materials, add into reaction mixture

Incubate:

30 C for 15 min

50 C for 15 min

55 C for 15 min

25 C for 10 min

98 C for 2 min

4 C hold (indefinitely)

Amplification

Materials

1 ul for each P1 and A-Barcode-universal primers optionally containing barcode sequence (Ion Xpress™ Adapters, Thermo Fisher Scientific)

Method

Add into the reaction wells the above materials, amplify:

99 C for 2 min

20 cycles:

-   -   99 C for 20 s     -   64 C for 20 s     -   72 C for 20 s

72 C for 5 min

4 C hold (indefinitely)

The resulting sample is purified using 1× Ampure® beads (Beckman Coulter, Inc.) according to the manufacturer instructions. Optionally, purification step may be repeated 1× to 2×.

Example 1D

Materials and Method

Optional Reverse Transcription (RT) Reaction method (10 uL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

2 uL 5× SuperScript™ VILO™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤8 uL volume of DNA+RNA sample for ≤20 ng total amount of DNA+RNA sample (˜1% RNA sample of the total nucleic acid (TNA));

nuclease-free H2O to the above tube/well to make 10 uL total reaction volume;

Method:

42 C for 30 min

85 C for 1 min

4 C hold (indefinitely)

Amplification:

Materials

_x_ul nuclease free dH₂O (x to 30 ul final) _y_ul Genomic DNA sample (y ~20 ng) or y 10 uL of RT reaction for DNA + RNA sample 12.5 ul Adaptor Panel for ~50 nM each primer concentration  7.5 ul Platinum ™  SuperFi ™  PCR master mix, replacing SuperFi enzyme with 0.96 U/μL SuperFiU ™  DNA Polymerase  3.0 ul 2 U/ul SuperFiU ™  DNA Polymerase

optionally, an control may be included in reaction, (e.g, Acrometrix Oncology Hotspot Control (Thermo Fisher Scientific))

Amplification

-   -   Assemble mixture of materials in reaction in 96-well plate         wells, seal, vortex and centrifuge plate, amplify using method:     -   99 C for 1 s     -   3 cycles of the following:         -   99 C for 30 s         -   64 C for 2 min         -   60 C for 6 min         -   72 C for 30 s     -   then 72 C for 2 min     -   4 C hold (indefinitely)

Digestion, Fill-in, Ligation:

Materials

0.1 ul VIP Oligo 0.2 uM (P/N 4385451 Thermo Fisher Scientific, Inc.) 2 ul (5 u/ul) UDG 4 ul (8 U/ul) APE1 (NEB, M0282L) 0.5 ul (0.1 U/ul) Taq polymerase (EP0404) 1 ul (6000 U/ul) T7 ligase (NEB M0318L) 1 ul (2 mM) ATP 0.5 ul mAB2A7 (0.6 mg/mL) 0.25 ul mAB5D3 (0.25 mg/mL)

Method

Mix the above materials, add into reaction mixture, seal plate, vortex and centrifuge

Incubate:

30 C for 15 min

50 C for 15 min

55 C for 15 min

25 C for 10 min

98 C for 2 min

4 C hold (indefinitely)

Amplification

Materials

1 ul for each P1 and A-Barcode-universal primers optionally barcoded sequence (Ion Xpress™ Adapters, Thermo Fisher Scientific); or 1 uL each of 10 uM BC1-Ah, and 1 uL of 10 uM P1-P1 h (IonCode™ Barcode Adapters, Thermo Fisher Scientific), for uni-directional library

Method

Add into the reaction wells the above materials, seal plate, vortex and centrifuge, then amplify:

99 C for 15s

5 cycles:

-   -   99 C for 15 s     -   62 C for 20 s     -   72 C for 20 s

15 cycles:

-   -   99 C for 15 s     -   70 C for 40 s

72 C for 5 min

4 C hold (indefinitely)

The resulting sample is purified using 1× Ampure® beads (Beckman Coulter, Inc.) according to the manufacturer instructions.

Optionally, purification may be repeated 1× to 2×.

Example 1E

Materials and Method

Amplification:

Materials

x_ul dH₂O (x to 30 ul final) y_ul Genomic DNA sample (y ~20 ng) or y 10 uL of RT reaction for DNA + RNA sample 12.5 ul Adaptor Panel for ~50 nM each primer concentration  7.5 ul Platinum ™  SuperFi ™  PCR master mix, replacing SuperFi enzyme with 0.96 U/μL SuperFiU ™  DNA Polymerase  3.0 ul 2 u/ul SuperFiU ™  DNA Polymerase

Amplification

-   -   Assemble mixture of materials in reaction in 96-well plate         wells, seal plate, vortex and centrifuge, then amplify using         method:     -   99 C for 1 s 3 cycles of the following:     -   99 C for 30 s         -   64 C for 2 min         -   60 C for 6 min         -   72 C for 30 s     -   72 C for 2 min     -   4 C hold (indefinitely)

Digestion, Fill-in, Ligation:

Materials

0.1 ul VIP Oligo 0.2 uM (P/N 4385451 Thermo Fisher Scientific, Inc.) 2 ul (5 u/ul) UDG 4 ul (8 U/ul) APE1 (NEB, M0282L) 0.5 ul (0.1 U/ul) Taq polymerase (EP0404) 1 ul (6000 U/ul) T7 ligase (NEB M0318L) 1 ul (2 mM) ATP 0.5 ul mAB2A7 (0.6 mg/mL) 0.25 ul mAB5D3 (0.25 mg/mL)

Method

Mix the above materials, add into reaction mixture, seal plate, vortex and centrifuge

Incubate:

30 C for 15 min

50 C for 15 min

55 C for 15 min

25 C for 10 min

98 C for 2 min

4 C hold (indefinitely)

Amplification

Materials

1 uL of 10 uM BC1-Ah, 1 uL of 10 uM P1-Uh, 1.5 uL of 10 uM BC1-Uh, and 1.5 uL of 10 uM P1-Ah. herein for bi-directional library preparation. BC1-Ah comprises barcode sequence and complementary sequence to universal A handle of forward adapters herein; BC1-Uh comprises barcode sequence and complementary sequence to universal handle of any of reverse adapters B, C, D, or E herein; P1-Uh comprises Ion adapter P1 adapter sequence, barcode sequence, and complementary sequence to universal B, C, D, or E handle of any of reverse adapters B, C, D, or E herein; P1-Ah comprises Ion adapter P1 adapter sequence, barcode sequence, and complementary sequence to universal handle of A handle of forward adapters herein. See FIG. 7.

Method

Add into the reaction wells the above materials, seal plate, vortex, centrifuge then amplify:

99 C for 15 s

5 cycles:

-   -   99 C for 15 s     -   62 C for 20 s     -   72 C for 20 s

15 cycles:

-   -   99 C for 15 s     -   70 C for 40 s

72 C for 5 min

4 C hold (indefinitely)

The resulting sample is purified using 1× Ampure® beads (Beckman Coulter, Inc.) according to the manufacturer instructions.

Optionally, purification may be repeated 1× to 2×.

Example 1F

Materials and Method

Optional Reverse Transcription (RT) Reaction method (10 uL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

2 uL 5× SuperScript™ VILO™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤8 uL volume of DNA+RNA sample for ≤20 ng total amount of DNA+RNA sample (˜1% RNA sample of the total nucleic acid (TNA));

nuclease-free H2O to the above tube/well to make 10 uL total reaction volume;

Method:

42 C for 30 min

85 C for 1 min

4 C hold (indefinitely)

Amplification:

Materials

_x_ul nuclease free dH₂O (x to 30 ul final) _y_ul Genomic DNA sample (y ~20 ng) or y 10 uL of RT reaction for DNA + RNA sample 12.5 ul Adaptor Panel for ~50 nM each primer concentration  7.5 ul Platinum ™  SuperFi ™  PCR master mix, replacing SuperFi enzyme with 0.96 U/μL SuperFiU ™  DNA Polymerase  3.0 ul 2 U/ul SuperFiU ™  DNA Polymerase

optionally, a control may be included in reaction, (e.g, Acrometrix Oncology Hotspot Control (Thermo Fisher Scientific))

Amplification

-   -   Assemble mixture of materials in reaction in 96-well plate         wells, seal, vortex and centrifuge plate, amplify using method:     -   99 C for 1 s     -   3 cycles of the following:         -   99 C for 30 s         -   64 C for 2 min         -   60 C for 6 min         -   72 C for 30 s     -   then 72 C for 2 min     -   4 C hold (indefinitely)

Digestion, Fill-in, Ligation:

Materials

0.1 ul VIP Oligo 0.2 uM (P/N 4385451 Thermo Fisher Scientific, Inc.) 2 ul (5 u/ul) UDG 4 ul (8 U/ul) APE1 (NEB, M0282L) 0.5 ul (0.1 U/ul) Taq polymerase (EP0404) 1 ul (6000 U/ul) T7 ligase (NEB M0318L) 1 ul (2 mM) ATP 0.5 ul mAB2A7 (0.6 mg/mL) 0.25 ul mAB5D3 (0.25 mg/mL)

Method

Mix the above materials, add into reaction mixture, seal plate, vortex and centrifuge

Incubate:

30 C for 15 min

50 C for 15 min

55 C for 15 min

25 C for 10 min

98 C for 2 min

4 C hold (indefinitely)

Amplification

Materials

1 ul for each of (1) P5-index-A-handle primer; (2) P5-index-I-handle primer; (3) P7-index-A-handle primer; and (4) P7-index-I-handle primer. See Table F.

Method

Add into the reaction wells the above materials, seal plate, vortex and centrifuge, then amplify:

99 C for 15 s

5 cycles:

-   -   99 C for 15 s     -   62 C for 20 s     -   72 C for 20 s

15 cycles:

-   -   99 C for 15 s     -   70 C for 40 s

72 C for 5 min

4 C hold (indefinitely)

The resulting sample is purified using 1× Ampure® beads (Beckman Coulter, Inc.) according to the manufacturer instructions.

Optionally, purification may be repeated 1× to 2×.

Example 2

The first step of provided methods comprises a few rounds of amplification, for example, three to six cycles of amplification, and in certain instances, three cycles of amplification using forward and reverse adaptors to each gene specific target sequence. Each adaptor contains a 5′universal sequence, and a 3′ gene specific target sequence. In some embodiments adaptors optionally comprise a unique tag sequence located between the 5′ universal and the 3′ gene specific target sequences.

In specific embodiments wherein unique tag sequences are utilized, each gene specific target adaptor pair includes a multitude of different unique tag sequences in each adaptor. For example, each gene specific target adaptor comprises up to 4096 TAGS. Thus, each target specific adaptor pair comprises at least four and up to 16,777,216 possible combinations.

Each of the provided adaptors comprises a cleavable uracil in place of thymine at specific locations in the forward and reverse adaptor sequences. Positions of uracils (Us) are consistent for all forward and reverse adaptors having unique tag sequences, wherein uracils (Us) are present flanking the 5′ and 3′ ends of the unique tag sequence when present; and Us are present in each of the gene specific target sequence regions, though locations for each gene specific target sequence will inevitably vary. Uracils flanking each unique tag sequence (UT) and in gene-specific sequence regions are designed in conjunction with sequences and calculated Tm of such sequences, to promote fragment dissociation at a temperature lower than melting temperature of the universal handle sequences, which are designed to remain hybridized at a selected temperature. Variations in Us in the flanking sequences of the UT region are possible, however designs keep the melting temperature below that of the universal handle sequences on each of the forward and reverse adaptors. Exemplary adaptor sequence structures comprise:

Forward Adaptor: SEQ ID NO: 1 ------A Handle----- ------*UT*------ --Gene Specific-- TCTGTACGGTGACAAGGCG-U-NNNACTNNNTGA-U-GAGGACCGUCGCTUGGT Rev Adaptor B SEQ ID NO: 2 CTCTATGGGCAGTCGGTGAT-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----B Handle------- --------*UT*---- -------Gene Specific------- Rev Adaptor C SEQ ID NO: 3 TCTAGTCGGTCAGTCACGG-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----C Handle------- ------UT------- -------Gene Specific------- Rev Adaptor D SEQ ID NO: 4 TCTAGTGCTGCAGTCACGG-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----D Handle------- ------UT------- -------Gene Specific------- Rev Adaptor E SEQ ID NO: 5 TGACAAGGCGTAGTCACGG-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----E Handle------- ------UT------- -------Gene Specific------- Wherein each N is a base selected from A, C, G, or T and the constant sections of the UT region are used as anchor sequences to ensure correct identification of variable (N) portion. The constant and variable regions of the UT can be significantly modified (e.g., alternative constant sequence, >3 Ns per section) as long as the Tm of the UT region remains below that of the universal handle regions. Importantly, cleavable uracils are absent from each forward (e.g., TCTGTACGGTGACAAGGCG (SEQ ID NO:6) and reverse (e.g., CTCTATGGGCAGTCGGTGAT (SEQ ID NO:7) universal handle sequence.

Enzymes used for amplification include (but are not limited to): Phusion U DNA polymerase; SuperFi U DNA polymerase; Taq DNA polymerase; Veraseq Ultra DNA polymerase. SuperFi U DNA Polymerase is a modified version of high fidelity SuperFi DNA Polymerase, available from Thermo Fisher Scientific. SuperFiU DNA comprises a modification in the uracil-binding pocket (e.g., AA 36) and a family B polymerase catalytic domain (e.g., AA 762). SuperFiU is described in U.S. Provisional patent application No. 62/524,730 filed Jun. 26, 2017, and International Patent application no. PCT/EP2018/066896, filed Jun. 25, 2018 which are each hereby incorporated by reference. Polymerase enzymes may be limited in their ability to utilize uracil and/or any alternative cleavable residues (e.g., inosine, etc.) included into adaptor sequences. In certain embodiments, it may also be advantageous to use a mixture of polymerases to reduce enzyme specific PCR errors.

The second step of methods involves partial digestion of resulting amplicons, as well as any unused uracil-containing adaptors. For example, where uracil is incorporated as a cleavable site, digestion and repair includes enzymatic cleavage of the uridine monophosphate from resulting primers, primer dimers and amplicons, and melting DNA fragments, then repairing gapped amplicons by polymerase fill-in and ligation. This step reduces and potentially eliminates primer-dimer products that occur in multiplex PCR. In some instances, digestion and repair are carried out in a single step. In certain instances, it may be desirable to separate digestion and repair-steps temporally. For example, thermolabile polymerase inhibitors may be utilized in conjunction with methods, such that digestion occurs at lower temperatures (25-40° C.), then repair is activated by increasing temperature enough to disrupt a polymerase-inhibitor interaction (e.g., polymerase-Ab), though not high enough to melt the universal handle sequences.

Uracil-DNA Glycosylase (UDG) enzyme can be used to remove uracils, leaving abasic sites which can be acted upon by several enzymes or enzyme combinations including (but not limited to): APE 1-Apurinic/apyrimidinic endonuclease; FPG-Formamidopyrimidine [fapy]-DNA glycosylase; Nth-Endonuclease III; Endo VIII-Endonuclease VIII; PNK-Polynucleotide Kinase; Taq- Thermus aquaticus DNA polymerase; DNA pol I-DNA polymerase I; Pol beta-Human DNA polymerase beta. In a particular implementation, the method uses Human apurinic/apyrimidinic endonuclease, APE1. APE1 activity leaves a 3′-OH and a 5′deoxyribose-phosphate (5′-dRP). Removal of the 5′-dRP can be accomplished by a number of enzymes including recJ, Polymerase beta, Taq, DNA pol I, or any DNA polymerase with 5′-3′ exonuclease activity. Removal of the 5′-dRP by any of these enzymes creates a ligatable 5′-phosphate end. In another implementations, UDG activity removes the Uracil and leaves and abasic site which is removed by FPG, leaving a 3′ and 5′-phosphate. The 3′-phosphate is then removed by T4 PNK, leaving a polymerase extendable 3′-OH. The 5′-deoxyribose phosphate can then be removed by Polymerase beta, fpg, Nth, Endo VIII, Taq, DNA pol I, or any other DNA polymerase with 5′-3′ exonuclease activity. In a particular implementation Taq DNA polymerase is utilized.

Repair fill-in process can be accomplished by almost any polymerase, possibly the amplification polymerase used for amplification in step 1 or by any polymerase added in step 2 including (but not limited to): Phusion DNA polymerase; Phusion U DNA polymerase; SuperFi DNA polymerase; SuperFi U DNA polymerase; TAQ; Pol beta; T4 DNA polymerase; and T7 DNA polymerase. Ligation repair of amplicons can be performed by many ligases including (but not limited to): T4 DNA ligase; T7 DNA ligase; Taq DNA ligase. In a particular implementation of the methods, Taq DNA polymerase is utilized and ligation repaired in accomplished by T7 DNA ligase.

A last step of library preparation involves amplification of the repaired amplicons by standard PCR protocols using universal primers that contain sequences complementary to the universal handle sequences on the 5′ and 3′ ends of prepared amplicons. For example, an A-universal primer, and a P1 universal primer, each part of the Ion Express Adaptor Kit (Thermo Fisher Scientific, Inc.) may optionally contain a sample specific barcode. The last library amplification step may be performed by many polymerases including, but not limited to: Phusion DNA polymerase; Phusion U DNA polymerase; SuperFi DNA polymerase; SuperFi U DNA polymerase; Taq DNA polymerase; Veraseq Ultra DNA polymerase.

2A, In one specific implementation, adaptors were designed using the composition design approach provided herein, including universal handle-unique tag-gene specific target sequence described in Example 2 above, and targeted to genes using the ONCOMINE™ Focus Research Panel (Thermo Fisher Scientific, Inc.) target sequences and ION AMPLISEQ™ Designer (Thermo Fisher Scientific, Inc). Forward and reverse adaptors described above were utilized comprising

Forward Adaptor: SEQ ID NO: 1 ------A Handle----- ------*UT*------ --Gene Specific-- TCTGTACGGTGACAAGGCG-U-NNNACTNNNTGA-U-GAGGACCGUCGCTUGGT Rev Adaptor B SEQ ID NO: 2 CTCTATGGGCAGTCGGTGAT-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----B Handle------- --------*UT*---- -------Gene Specific------- With target sequences specific to targets as in Table A, and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Preparation of library was carried out according to the method described above for Example 1A. Formamidopyrimidine [fapy]-DNA glycosylase (FPG)/UDG enzyme is utilized for digestion, which is expected to create abasic sites at all uracil positions, FPG is expected to cleave on the 5′ and 3′ side of the abasic site (leaving a 3′-phosphate and a 5′ phosphate) and removal of the 3′phosphate (by T4 PNK for example) should produce an extendable 3′-OH and a ligatable 5′-phosphate. However, as shown by the BioAnalyzer trace (See FIG. 2), this process consistently failed to generate recoverable product. The process can be rescued however by the addition of an additional purification step post-repair. The purification process can be anything inactivates and removes the repair enzymes prior to the next amplification step. Similar results were obtained if endoVIII was utilized.

2B. In another specific implementation, adaptors were prepared as described in section 2A for targets of the ONCOMINE™ Focus Assay. See Table B. Forward and reverse adaptors described above were utilized comprising

Forward Adaptor: SEQ ID NO: 1 ------A Handle----- ------*UT*------ --Gene Specific-- TCTGTACGGTGACAAGGCG-U-NNNACTNNNTGA-U-GAGGACCGUCGCTUGGT Reverse Adaptor was any of Rev Adaptor B, Rev Adaptor C, Rev Adaptor D, Rev Adaptor E: Rev Adaptor B SEQ ID NO: 2 CTCTATGGGCAGTCGGTGAT-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----B Handle------- --------*UT*---- -------Gene Specific------- Rev Adaptor C SEQ ID NO: 3 TCTAGTCGGTCAGTCACGG-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----C Handle------- ------UT------- -------Gene Specific------- Rev Adaptor D SEQ ID NO: 4 TCTAGTGCTGCAGTCACGG-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----D Handle------- ------UT------- -------Gene Specific------- Rev Adaptor E SEQ ID NO: 5 TGACAAGGCGTAGTCACGG-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----E Handle------- ------UT------- -------Gene Specific------- With target sequences specific to targets as in Table B, and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Preparation of library was carried out according to the method described above for 1C. See FIG. 3, Table 1. Similar successful sequencing results were generated with each of the reverse adaptor pairings.

Example 3

Prepared libraries are sequenced, and analyzed. Sequencing can be carried out by a variety of known methods, including, but not limited to sequencing by synthesis, sequencing by ligation, and/or sequencing by hybridization. Sequencing has been carried out in the examples herein using the Ion Torrent platform (Thermo Fisher Scientific, Inc.), however, libraries can be prepared and adapted for analysis, e.g., sequencing, using any other platforms, e.g., Illumina, PacBio, etc. Result may be analyzed using a number of metrics to assess performance, for example:

-   -   #of families (with ng input DNA captured) The median #of         families is a measure of the number of families that maps to an         individual target. In this case, each unique molecular tag is a         family.     -   Uniformity is a measure of the percentage of target bases         covered by at least 0.2× the average read depth. This metric is         used to ensure that the technology does not selectively         under-amplify certain targets.     -   Positives/Negatives: When a control sample with known mutations         is utilized is analyzed (e.g., Acrometrix Oncology Hotspot         Control DNA, Thermo Fisher Scientific, Inc.), the number of True         Positives can be tracked.         -   True Positives: The number of True Positives informs on the             number of mutations that were present and correctly             identified.         -   False positives (FP): (Hot spot and Whole Target) The number             of False Positives informs on the number of mutations that             are determined to be present, but known not to be in the             sample.         -   False negatives (FN) (if acrometrix spike-in is used) The             number of False Negatives informs on the number of mutations             that were present but not identified.     -   On/Off Target is the percentage of mapped reads that were         aligned/not aligned over a target region. This metric is used to         ensure the technology amplifies predominantly the targets to         which the panel was designed.     -   Low quality is tracked to ensure the data is worth analyzing.         This metric is a general system metric and isn't directly         related to this technology.

Example 4

One benefit of the instant invention is the ability to use Ampliseq.com designer in conjunction with the provided methodology. Adaptors were designed using the composition design approach provided herein, including universal handle-unique tag-gene specific target sequence described in Example 2 above, and targeted to genes using the ONCOMINE™ Focus Research Panel (Thermo Fisher Scientific, Inc.) target sequences and ION AMPLISEQ™ Designer (Thermo Fisher Scientific, Inc). Forward and reverse adaptors described above were utilized comprising

Forward Adaptor: SEQ ID NO: 1 ------A Handle----- ------*UT*------ --Gene Specific-- TCTGTACGGTGACAAGGCG-U-NNNACTNNNTGA-U-GAGGACCGUCGCTUGGT Rev Adaptor B SEQ ID NO: 2 CTCTATGGGCAGTCGGTGAT-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----B Handle------- --------*UT*---- -------Gene Specific------- With target sequences specific to targets as in Table A, and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Library was prepared using 20 ng of genomic DNA and ˜1% Acrometrix Oncomine™ Hotspot Control (AOHC) DNA (Thermo Fisher Scientific, Inc.), according to the protocol described above in Example 1C. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). Performance with the panel (eg., yield, uniformity) indicates the technology is able to effectively make use of the designer pipeline. See FIG. 4A-4C.

Results using the AOHC DNA (shown in Table 1) demonstrate that, using this protocol, we effectively identify most of the True Positives (71 or 75) present in the AOHC and importantly did not generate any False positives.

TABLE 1 Oncology BRCA Panel Oncology HotSpot Oncology HotSpot Panel (Ex 4) (Ex 5) Panel (Ex 3) Bidirectional (ex 6) True Positives   75 NA NA NA TP in SNP, INDEL 71; 4 NA NA NA False Negatives    3 NA NA NA False Positives    0   0   0   0 Uniformity 98.60%  100%  100%  100% Low Quality   15%  28%  31%  26% On Target   98%  95%  96%  95% # of Families  4398 5208 8755 6391

Example 5

Adaptors were designed according to the composition design approach provided herein, including universal handle-unique tag-gene specific target sequence described in Example 2 above, and targeted to genes using the BRCA Research Panel (Thermo FisherScientific, Inc.) target sequences and ION AMPLISEQ™ Designer (Thermo Fisher Scientific, Inc). Forward and reverse adaptors described above were utilized comprising

Forward Adaptor: SEQ ID NO: 1 ------A Handle----- ------*UT*------ --Gene Specific-- TCTGTACGGTGACAAGGCG-U-NNNACTNNNTGA-U-GAGGACCGUCGCTUGGT Rev Adaptor B SEQ ID NO: 2 CTCTATGGGCAGTCGGTGAT-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----B Handle------- --------*UT*---- -------Gene Specific-------

With target sequences specific to targets as in Table C, and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Library was prepared using 20 ng genomic DNA according to the protocol described above in Example 1C Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). Similar to Example 5, performance (e.g., yield, uniformity) with the panel indicates the technology is able to use the designer pipeline. See FIG. 5 and Table 1.

Example 6

Primers were designed using the composition design approach provided herein and targeted to oncology genes using those of the panel target sequences as described above in Example 4, except that the library amplification step utilized two primer pairs (to put the two universal sequences on each end of amplicons, e.g., an A-universal handle and a P1-universal handle on each end) to enable bi-directional sequencing. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). See FIG. 7. Performance (e.g., yield, uniformity) with the instant panel indicates the technology is able to use the designer pipeline and effectively generate sequencing data for both strands of DNA. See FIG. 6A-6C and Table 1.

Example 7

Primers were designed using the composition design approach provided herein and targeted to a wide variety of oncology target sequences. Forward and reverse adaptors described above were utilized comprising

Forward Adaptor: SEQ ID NO: 1 ------A Handle----- ------*UT*------ --Gene Specific-- TCTGTACGGTGACAAGGCG-U-NNNACTNNNTGA-U-GAGGACCGUCGCTUGGT Rev Adaptor C SEQ ID NO: 3 TCTAGTCGGTCAGTCACGG-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----C Handle------- ------UT------- -------Gene Specific-------

TABLE 2A Family Generation, Coverage, and Uniformity AmpliSeq HD Median Read Median # Median # Counts per Uniformity Families Molecular Families Sample Input Target (U50) Size >= 3 Conversion Size >= 3 cfDNA 2016B 20 ng 61,939 95.9% 5794 48% 5794 63,679 95.9% 5879 49% 5879 cfDNA 416G 20 ng 79,004 98.6% 7676 64% 7676 61,694 98.6% 7322 61% 7322 0.5% fMM 6000 copies 61,458 98.6% 5466 46% 5466 62,019 98.6% 5685 47% 5685 0.1% fMM 6000 copies 70,397 98.6% 6278 52% 6278 60,879 98.6% 5946 50% 5946 gDNA 292 copies 22,650 97.3% 340 57% 340 79,746 98.6% 354 59% 354

TABLE 2B Sensitivity, Specificity, and FPs/lib, Hot Spots Only AmpliSeq HD Sample Input Sensitivity (%) Specificity (%) FP cfDNA 2016B 20 ng 100.00 0 99.70 1 cfDNA 416G 20 ng 100.00 0 100.00 0 0.5% allelic 6000 copies 100.0 100.00 0 Frequency 100.0 100.00 0 0.1% allelic 6000 copies 85.14 100.00 0 Frequency 94.60 100.00 0 gDNA 292 copies 100.00 0 100.00 0

With target sequences specific to targets as in Table D and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Samples containing 19.8 ng of cell free DNA and 0.2 ng of total RNA were processed as described in example 1D, starting with the optional reverse transcriptase step. Total RNA for some samples listed contained 5 spiked in fusion constructs. See Table D. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). Performance (e.g., yield, uniformity, molecular conversion, sensitivity) with the instant panel indicates the technology can efficiently convert input DNA into library and detect mutations present at frequencies as low as 0.1% to 0.5%. See Table 2A-2B. Additionally, results confirm the technology can efficiently convert input DNA and cDNA into library and detect fusions present at frequencies of ˜1%. See Table 3A-3B.

TABLE 3A Fusions LRIG3-ROS1 EZR-ROS1 KLC1-ALK CCDC6-RET GOPC-ROS1 SDC4-ROS1 CD74-ROS1 HIP1-ALK SLC34A2-ROS1 CUX1-RET KIF5B-ALK TPM3-ROS1 EML4-ALK KIF5B-RET TPR-ALK

TABLE 3B Family Generation, Coverage, and Uniformity (No Activation) Sample Input FP U50 Conversion cfDNA 5022 10 ng 0 (343) 98.5 44% 0 (323) cfDNA 5022 + 10 ng 0 (343) 99.25 51% total RNA 2 (323) cfDNA 5022 + 10 ng 0 (343) 98.5 50% Trifusion 1 (323) gDNA 10 ng 0 (343) 93.98 45% 2 (323) gDNA + 10 ng 0 (343) 93.98 54% total RNA 0 (323) gDNA + 10 ng 1 (343) 95.49 53% Trifusion 1 (323)

Example 8

Primers were designed using the composition design approach provided herein and targeted to genes using those of short tandem repeats (STRs), which are useful for high resolution genotyping and analysis of complex mixtures. Forward and reverse adaptors described above were utilized comprising

Forward Adaptor: SEQ ID NO: 1 ------A Handle----- ------*UT*------ --Gene Specific-- TCTGTACGGTGACAAGGCG-U-NNNACTNNNTGA-U-GAGGACCGUCGCTUGGT Rev Adaptor E SEQ ID NO: 5 TGACAAGGCGTAGTCACGG-U-NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----E Handle------- ------UT------- -------Gene Specific-------

With target sequences specific to targets as in Table E and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Samples containing 1 to 10 ng of genomic DNA were processed as described in example 1D without the optional reverse transcriptase step. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). Performance (e.g., yield, uniformity) with the instant panel indicates that even challenging STR targets (which are often shortened by 1 or more repeats during amplification) can be efficiently converted into a library. Results were consistent across titration levels of input DNA. See Table 4. When results were compared to standard operating procedure according to manufacturer instructions using Torrent Suite Molecular Diagnostics plugin to evaluate the same targets, results generated using compositions and methods provided herein yielded more consistent signal over each of the repeat regions, with less stutter (data not shown).

TABLE 4 Half-Double 80% Median Read Median # Uniformity Uniformity Barcode Input Counts per Families (Families (Families Name DNA Target Size >= 3 Size >= 3) Size >= 3) BC_0102  1 ng 37,727 257 77.78% 63.89% BC_0105  2 ng 35,056 412 83.33% 63.89% BC_0108  5 ng 32,478 1021 80.56% 69.44% BC_0120 10 ng 30,915 1646 86.11% 63.89%

Example 9

Primers were designed using the composition design approach provided herein and targeted to oncology genes target sequences as described above in Example 6, where two primer pairs were utilized in library amplification (to put the two universal sequences on each end of amplicons, e.g., an A-universal handle and a P1-universal handle on each end) to enable bi-directional sequencing. Library preparation was carried out on samples containing spiked in AOHC control as described according to methods of Example 1E above without optional RT step. See FIG. 7. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.), then analyzed separately for unidirectional sequence results as well as results analyzed from bidirectional sequencing. Performance (e.g., yield, uniformity, sensitivity) with the instant panel indicates the technology is able to use the designer pipeline and effectively generate sequencing data for both strands of DNA, and bidirectional sequence analysis results in reduction of indel False Positives measured. See Table 5.

TABLE 5 Bidirectional, Bidirectional, Analyzed Analyzed Unidirectional Bidirectional True Positives 67 67 Sensitivity 91.8 91.8 TP in SNP, INDEL 65; 2 65; 2 False Negatives 6 6 False Positives in SNP, INDEL 1:2 1:0

Example 10

For each of the Ion barcode adaptors, a single barcode is included in an A adapter. Addition of a second set of barcodes on the P1 adapter can effectively reduce the level of contamination artifacts in results by filtering out identified contamination reads. Primers were designed using the composition design approach provided herein and targeted to a wide variety of oncology target sequences. Samples containing 20 ng of genomic DNA were processed similarly to those described in Example 7 above and using the method of example 1D, however, additionally barcoded P1 adapters were also utilized, wherein a barcode 12mer sequence was inserted into the P1 adapter sequence of the reverse adapator. Sample containing genomic DNA for library preparation was processed with barcode 8 in both A and P1 adapters. Additional samples were also processed with barcodes 1, 2, 3, 4, 5, 6, 7 and 9 (each in both P1 and A barcoded adapters), but without genomic DNA. Performance (e.g., yield, uniformity, Conversion) with the instant panel indicates that additional barcodes can effectively identify contamination. See Table 6.

TABLE 6 Reverse Barcode Reads Detected % Total bc1 332  0.001% bc2 54  0.000% bc3 261  0.001% bc4 481  0.001% bc5 9,908  0.019% bc6 8,532  0.016% bc7 2,656  0.005% bc8 52,089,480 99.941% bc9 1,403  0.003% bc10 7,131  0.014%

Example 11

In another specific implementation, adaptors were prepared as described in example 2A for targets of the ONCOMINE™ Focus Assay, as in Table B, as well as described in example 6 with target sequences specific to targets as in Table D and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Forward and reverse adaptors utilized comprising

Forward Adaptor: SEQ ID NO: 1 ------A Handle------ ------*UT*---- ---Gene Specific-- TCTGTACGGTGACAAGGCG- U -NNNACTNNNTGA- U -GAGGACCGUCGCTUGGT Rev Adaptor I: SEQ ID NO: 1705 TGACAAGGCGTAGTCACGG - U -NNNACTNNNTGA-U-CCTTCTGCAUGGTATTCTTTCTCTUCC -----I Handle---------------*UT*---- -------Gene Specific-------

Preparation of library was carried out according to the method described above for 1F. See also FIG. 8. The workflow has been adapted to use amplification primers to enable libraries to carry out sequencing runs on the Illumina platform. The design (shown schematically in FIG. 8) contains: (1) P5 grafting primer region; (2) P5 index (A-H) region; (3) P5 sequencing/index read primer region; (4) A-handle region; (5) UT region; (6) gene specific insert; (7) UT region; (8) I-handle region; (9) P7 sequencing/index read primer region; (10) P7 index (1-12) region; and (11) P7 grafting primer region. 3 libraries were made with an oncology panel comprising targets of Table D having idex5-01-idex7-5, idex5-02-index7-6 and idex5-7-idex7-7 respectively. 2 libraries were made with Focus panel comprising targets of Table B having idex5-01-idex7-5, and idex5-7-idex7-7 respectively. See Table F. All libraries are made with 19.6 ng of g24385 with 0.4 ng spike-in AOHC so we could detect 0.1% allele frequency.

TABLE F Name Sequence (5′ to 3′) SEQ ID 5-01-Ah AATGATACGGCGACCACCGAGATCTACAC AGCGCTAG TCGTCGGCAGCGTC 1706 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 5-02-Ah AATGATACGGCGACCACCGAGATCTACAC GATATCGA TCGTCGGCAGCGTC 1707 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 5-07-Ah AATGATACGGCGACCACCGAGATCTACAC ACATAGCG TCGTCGGCAGCGTC 1708 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 5-08-Ah AATGATACGGCGACCACCGAGATCTACAC GTGCGATA TCGTCGGCAGCGTC 1709 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 5-09-Ah AATGATACGGCGACCACCGAGATCTACAC CCAACAGA TCGTCGGCAGCGTC 1710 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 5-010-Ah AATGATACGGCGACCACCGAGATCTACAC TTGGTGAG TCGTCGGCAGCGTC 1711 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 5-013-Ah AATGATACGGCGACCACCGAGATCTACAC AACCGCGG TCGTCGGCAGCGTC 1712 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 5-014-Ah AATGATACGGCGACCACCGAGATCTACAC GGTTATAA TCGTCGGCAGCGTC 1713 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 01-Ih AATGATACGGCGACCACCGAGATCTACAC AGCGCTAG TCGTCGGCAGCGTC 1714 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 02-Ih AATGATACGGCGACCACCGAGATCTACAC GATATCGA TCGTCGGCAGCGTC 1715 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 5-07-Ih AATGATACGGCGACCACCGAGATCTACAC ACATAGCG TCGTCGGCAGCGTC 1716 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 5-08-Ih AATGATACGGCGACCACCGAGATCTACAC GTGCGATA TCGTCGGCAGCGTC 1717 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 5-09-Ih AATGATACGGCGACCACCGAGATCTACAC CCAACAGA TCGTCGGCAGCGTC 1718 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 5-010-Ih AATGATACGGCGACCACCGAGATCTACAC TTGGTGAG TCGTCGGCAGCGTC 1719 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 5-013-Ih AATGATACGGCGACCACCGAGATCTACAC AACCGCGG TCGTCGGCAGCGTC 1720 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 5-014-Ih AATGATACGGCGACCACCGAGATCTACAC GGTTATAA TCGTCGGCAGCGTC 1721 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-1-Ah CAAGCAGAAGACGGCATACGAGAT ATATTCAC GTCTCGTGGGCTCGG 1722 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-2-Ah CAAGCAGAAGACGGCATACGAGAT GCGCCTGT GTCTCGTGGGCTCGG 1723 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-3-Ah CAAGCAGAAGACGGCATACGAGAT ACTCTATG GTCTCGTGGGCTCGG 1724 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-4-Ah CAAGCAGAAGACGGCATACGAGAT GTCTCGCA GTCTCGTGGGCTCGG 1725 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-5-Ah CAAGCAGAAGACGGCATACGAGAT AGTAGAGA GTCTCGTGGGCTCGG 1726 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-6-Ah CAAGCAGAAGACGGCATACGAGAT GACGAGAG GTCTCGTGGGCTCGG 1727 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-7-Ah CAAGCAGAAGACGGCATACGAGAT AGACTTGG GTCTCGTGGGCTCGG 1728 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-8-Ah CAAGCAGAAGACGGCATACGAGAT GAGTCCAA GTCTCGTGGGCTCGG 1729 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-9-Ah CAAGCAGAAGACGGCATACGAGAT AATTCTGC GTCTCGTGGGCTCGG 1730 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-10-Ah CAAGCAGAAGACGGCATACGAGAT GGCCTCAT GTCTCGTGGGCTCGG 1731 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-1-Ah CAAGCAGAAGACGGCATACGAGAT ATCTTAGT GTCTCGTGGGCTCGG 1732 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-12-Ah CAAGCAGAAGACGGCATACGAGAT GCTCCGAC GTCTCGTGGGCTCGG 1733 AGATGTGTATAAGAGACAG TCTGTACGGTGACAAGGCGT 7-1-Ih CAAGCAGAAGACGGCATACGAGAT ATATTCAC GTCTCGTGGGCTCGG 1734 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-2-Ih CAAGCAGAAGACGGCATACGAGAT GCGCCTGT GTCTCGTGGGCTCGG 1735 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-3-Ih CAAGCAGAAGACGGCATACGAGAT ACTCTATG GTCTCGTGGGCTCGG 1736 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-4-Ih CAAGCAGAAGACGGCATACGAGAT GTCTCGCA GTCTCGTGGGCTCGG 1737 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-5-Ih CAAGCAGAAGACGGCATACGAGAT AGTAGAGA GTCTCGTGGGCTCGG 1738 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-6-Ih CAAGCAGAAGACGGCATACGAGAT GACGAGAG GTCTCGTGGGCTCGG 1739 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-7-Ih CAAGCAGAAGACGGCATACGAGAT AGACTTGG GTCTCGTGGGCTCGG 1740 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-8-Ih CAAGCAGAAGACGGCATACGAGAT GAGTCCAA GTCTCGTGGGCTCGG 1741 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-9-Ih CAAGCAGAAGACGGCATACGAGAT AATTCTGC GTCTCGTGGGCTCGG 1742 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-10-Ih CAAGCAGAAGACGGCATACGAGAT GGCCTCAT GTCTCGTGGGCTCGG 1743 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-11-Ih CAAGCAGAAGACGGCATACGAGAT ATCTTAGT GTCTCGTGGGCTCGG 1744 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT 7-12-Ih CAAGCAGAAGACGGCATACGAGAT GCTCCGAC GTCTCGTGGGCTCGG 1745 AGATGTGTATAAGAGACAG TGACAAGGCGTAGTCACGGT

To mimic low level of mutant variants (0.1%) presence in DNA samples, we used purified genomic DNA and spiked in small quantity of AcroMetrix Oncology Hotpot Control plasmid. These samples are used as our control samples for the purpose of demonstrating the library preparation method and assessing the sensitivity and specificity for low levels mutant variants detection by this assay method. Bioanalyzer results matched library structure designs, and yield and purity of libraries were on par with those prepared on other methods described above. Similar successful sequencing results were generated with each of the adaptor pairings.

A MiSeq sequencing run successfully generated clusters, and produced sequencing and indexing reads. Sequencing results of the panel run on the Illumina MiSeq indicate similar performance as compared to the standard AmpliSeq HD version run on the Ion S5 using a 540 chip. See Table 7.

TABLE 7 MiSeq S5 540 Raw Read Accuracy (%) 99.31 99.27 Mapped Reads 12,994,280 17,855,575 Mean Depth 46,674 62,429 On-Target (%) 98.91 98.64 coverageAnalysis Uniformity (%) 97.86 97.98 Half-Double Uniformity (%) 86.62 83.64 0.1% MegaMix TP 140 138 0.1% MegaMix FN 11 13 0.1% MegaMix FP 58 38

While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

TABLE A Primer Primer Name SEQ ID Primer Sequence (target of primer A) Name SEQ ID Primer Sequence (target seq of primer B) F1 8 GCTCCCAGGCACUTGATGAUAC R1 104 ACAGAAUCACAUGCCACACAGT F2 9 TGTTGCCATTUCAGGGTTTCUGA R2 105 TTCCTTCUAAAAGGCCATGAAGATCUG F3 10 ACCAAUGCGAGGAAGAAAAACAAUC R3 106 TCTGAAGAACAUGTGUGAGCACA F4 11 TCTTCAGAAUCTTGTTGGCUGCAT R4 107 CCCAACCCACAUTTCCTTTATAGATGTUT F5 12 AGAGTTGCAUCCTTCCCTTCUCT R5 108 TGTTCCAACAGGAUCTGUCCAAAA F6 13 CTGGCAUGACGCAGTTTCTUC R6 109 CCAGTGTCTGUCCTTGCCTTUC F7 14 GATCAAAGAGACGAAGUCTCTUGCA R7 110 CUATGACAAGAAAAUGGACACCAACAAG F8 15 CTTGCCUAGACAGCACCGUAAT R8 111 AGGAGGAUAAAGACCTGGUCCAT F9 16 TGGTTTCTGGUGGGACCATTAUG R9 112 GTCCTCUGGATCTCTTCAUGCA F10 17 TTGAAAGAGAACACACUTACTCUCCAC R10 113 CTGAGACATTCCUATGTCCTGCUC F11 18 CTCTACCAGAGUTAATCAACTGAUGCA R11 114 TUGAUACAAAACAAGCCCACGAACT F12 19 TATCAACTGTCCUTGTTGGCAAAUCA R12 115 CCAGCCTAATCTUGTTTTTCTTATGTTCUG F13 20 GCAAATGACTUGCTATTATTGAUGGCA R13 116 GTTATAGATGGUGAAACCTGTTTGTUGG F14 21 GTGGGATCATAUTCATCTACAAAGUGGT R14 117 GATTACTGGTTUCCAACAGGTTCTUG F15 22 GGAGGTCAUGGCATCGAGUT R15 118 TATGGTCTUGGACATCCAGGAUCT F16 23 GTGAGGCAGUCTTTACUCACCT R16 119 TAGGAAATGCAUTTCCTTTCTUCCCA F17 24 GGGAAATGUGAGCCCTUGAGAT R17 120 CCTGTGGCUGTCAGTATTUGGA F18 25 ACTCTTGCUCCTTCCATCCTUG R18 121 GTTCATCCUGCTGGAGCUCAT F19 26 CCCAAUGCAGCGAACAATGTUC R19 122 GTAGCTGCTGAAAAUGTAACTTTGTAUCC F20 27 GATCAGGGCUTCCAUGAGGAAA R20 123 ACTCTGTAGGCUGCAGTTCUCA F21 28 CTCAAGAGUGAGCCACTTCTUACC R21 124 CTCCTCTTGUCTTCTCCTTUGCA F22 29 AGAATAAAACACAUACAAGTTGGAAATTTCUGG R22 125 CTTGTGAGTGGAUGGGTAAAACCUAT F23 30 ACCUGAGCCAAGGACTTTUACC R23 126 CGGACTGAAAGUATAACCTTCTTCTTUCC F24 31 TGTCAATTAGCUGGAACATCUGAAACT R24 127 GCATGTGAACAUTCTGCTTTTCAUGG F25 32 GTGCCCTATUACCTCAATCAUCCT R25 128 ACGCCTTCACCUTTAACACCUC F26 33 CCAGACAGAAAAGCGGCUGTUA R26 129 ACTTGGGAGGUATCCACAUCCT F27 34 CCTAGTAGAATGTTUACTACCAAATGGAAUGA R27 130 AGATTCATCTUGAAGAAGTTGAUGGAGG F28 35 TTTTTGAUGAAACAAGACGACTTTGUG R28 131 GAATAGGATATTGUATCATACCAATTTCUCGAT F29 36 CACAGCUACACCATATATGAAUGGAGA R29 132 CAGCATTTGACTTUACCTTATCAATGTCUC F30 37 GATCTATGTUCGAACAGGTATCUACCATG R30 133 ACTGCTAAACACTAAUATAACCTTTGGAAAUAT F31 38 GGGAAGAAAAGUGTTTTGAAATGTGTUT R31 134 CATTTTTCCAGATACUAGAGTGTCTGTGUA F32 39 TTTGAATCTTUGGCCAGTACCUCA R32 135 CATAAGAGAGAAGGUTTGACTGCCAUAAA F33 40 GACTAGCUAGAGACAATGAATUAAGGGAAAA R33 136 GAATCTCCATTTUAGCACTTACCTGUGA F34 41 CTGAGATGCACAAUAAAACAGTUAGCC R34 137 AGAATGTCAGTUAAGTTAATGAGCTTTUCCAT F35 42 GACAUTCUCAAACAGGAGAAGAAGGA R35 138 GCTTGATUCCAAGGACCATGATCUG F36 43 TCTTTTCTCAAGUTGGCCTGAAUCA R36 139 CAATTCCCAAAAUGAAGGTAGCUACAC F37 44 CAATCTTTTGAUGACATTGCATACATUCGA R37 140 GGAAGATCCAAUCCATTTTTGTTGUCC F38 45 GTATGCAGGCAUCCTCAGCUA R38 141 CGGGAAGCGGGAGAUCTUG F39 46 CUGGUGACCGAGGACAACGT R39 142 GGCGTCCUACTGGCAUGA F40 47 GTCCUGGGAGTCUCAGGACA R40 143 CCTUCAGCAGCTUGAAGAGCT F41 48 CCAGTTACCUGTCCTGGTCAUT R41 144 GGAAACTCCCAUCTTGAGTCAUAAGG F42 49 AGTGAAAAACAAGCUCTCATGTCUGA R42 145 CATGTGTCCAGUGAAAATCCUCACT F43 50 GGAAAAATTGUGAAGATCTGTGACTTUGG R43 146 CTGACTUTAGAGATTAAAGUGAAGGAGGAT F44 51 AGCACTCTGACAUATGGCCATUT R44 147 CCTGGACAAAAAUACCAATCTATTGUGG F45 52 GGCACGGTUGAATGTAAGGCTUA R45 148 ACTGATATGGUAGACAGAGCCUAAACAT F46 53 CCCACAGAAACCCAUGTAUGAAGT R46 149 ACTGACCAAAACUCAGCCTGUT F47 54 TUGACAGAACGGGAAGCCCUCAT R47 150 CCTGACAGACAAUAAAAGGCAGCUT F48 55 CCTTACTCAUGGTCGGAUCACAA R48 151 GTTGAAACUAAAAATCCTTUGCAGGACT F49 56 CCAATATTATGGAUCCCAACTGCCUA R49 152 ACATTCTGAAGCAGCUTGGAGTUT F50 57 GCTACTTTGAUTTCTCCACTUCCAAC R50 153 GAGGAGATTGAAAAUCTTCCTGCCUT F51 58 AAAGGCAUGGAGCATCTGUACA R51 154 TTGGTCCGUCTCCUCCACGG F52 59 GTTATGTCCUCATTGCCCUCAACA R52 155 CTTCAGTCCGGUTTTATTTGCATCAUAG F53 60 CGAGGGCAAAUACAGCTTUGGT R53 156 GACTCTCCAAGAUGGGATACUCCA F54 61 TGATGGAGAUGTGATAATTUCAGGAAACA R54 157 CGGTGACTUACTGCAGCTGTUT F55 62 GAGACATGCAUGAACATTTTTCUCCA R55 158 TCCAGACCAGGGUGTTGTTTUC F56 63 GCCTCTUACACCCAGUGGAGAA R56 159 TGTGCCAGGGACCUTACCTTAUA F57 64 CCTTCTCUCTCTGTCAUAGGGACT R57 160 CACAGCAAAGCAGAAACUCACAUC F58 65 CTCCAGGAAGCCUACGTGAUG R58 161 TGTGTUCCCGGACATAGUCCA F59 66 CAGGAACGUACTGGUGAAAACAC R59 162 GAAAATGCUGGCTGACCUAAAGC F60 67 GCTTGTAAGUGCCCGAAGTGUA R60 163 CACAACCCACUGAGGTATATGTATAGGUAT F61 68 CGCAGTGCUAACCAAGTTCTTUC R61 164 CCATGGTTAAATAAAAUGCCACTTACTGUT F62 69 CAGTCAAGGUTGCTGATTTUGGT R62 165 CTTGGTGGUAAACTTTTGAGTTUGCA F63 70 CGAATCGCUACCCTGCTGUT R63 166 CCAAGCCUCATGGUGCCAT F64 71 TACCGAUACCGUGCGGG R64 167 TACUGGCAGCAAGUGCCCAG F65 72 CTGTCCUCCACAGGCATTTTUG R65 168 CCCTCACUCACAGCACATAGUC F66 73 CCATCCCUGACTGTGAGAUCAA R66 169 CCAGGUACGCCTCCAGAUGA F67 74 TCAGTGGAAAAAUAGCCTCAATTCTUACC R67 170 CTTCATGAAGACCUCACAGTAAAAAUAGGT F68 75 TATTATGACTUGTCACAATGUCACCACAT R68 171 GACTCGAGTGAUGATTGGGAGATUC F69 76 TTCCUTAGTCTTTCTTUGAAGCAGCA R69 172 AGATGCTCUGAGAAAGGCATUAGAAAG F70 77 TCTGACUCCACGAGAACTTGAUCATA R70 173 TATTGTTAACCUTGCAGAATGGUCGA F71 78 CAAGGCAUAAAAGCTGGGAAAUAGG R71 174 CUACCTGCCUACGCAACAAGAT F72 79 GGCTAUGGCACCUGCAACT R72 175 GGGACCUCAGATGTGCTGTUG F73 80 CCACAGAUCCACTGUGCGAC R73 176 GTGGCTTGUGGGCAAACTUG F74 81 CCATCCTGACCUGGTATGGUCA R74 177 CCTGCTUCAGGACGTTGAACUC F75 82 CAGCTCGTUCATCGGGACUT R75 178 ACCTGGCUCCTCTTCACGUA F76 83 CCTCCTTCCUAGAGAGTTAGAGUAACT R76 179 CACCCACACUTACACATCACTTUG F77 84 CACTGTGTTACUGCCATCGACTUA R77 180 TCGAGATTUAGCAGCCAGAAATGTUT F78 85 GATTCAATCAAACUGCAGAGTATTUGGG R78 181 TGATCTGGUGTCAGAGAUGGAGAT F79 86 GGCTTCTTGGUCGTGTTCTUCA R79 182 CUAGCGCCUGGAAGAGAAAAGGAGAT F80 87 CCCAGCGUCCTCAAAAGTUACA R80 183 CCCTCCACAAUCATTCCTGUGT F81 88 CTCTACGUCTCCUCCGACCA R81 184 CTTATTTATTGGTCUCTCATTCTCCCAUCC F82 89 CCTGTACTGGUGGATGTCCUCA R82 185 GCCTGTUGGACATCCTGGAUAC F83 90 CGCCAGGCUCACCTCTAUAG R83 186 AGGAGCGAUGACGGAATAUAAGC F84 91 TGTCTTTGCUGATGTTTCAAUAAAAGGAA R84 187 AGTTAAGGACTCUGAAGATGTACCTAUGG F85 92 CATGTACTGGUCCCTCATUGCA R85 188 GTAATAATCCAGACUGTGTTTCTCCCUT F86 93 TACCTCTATTGTUGGATCATATTCGUCCA R86 189 TATTATAAGGCCUGCTGAAAATGACUGAAT F87 94 CAGACACTGUACAAGCTCUACGA R87 190 GAAUAAAGAGGAGCAGGTUGAGGAA F88 95 CTCTGUCACAGTGGATUCGAGA R88 191 CAACATGACGAAGAUGGCAAACTUC F89 96 TCCUTCCATAGUGACCAAGACCA R89 192 GGGTACAUACAAAGCAGTCTGUGT F90 97 GGTTCCATUGGTAGCTGGUGAT R90 193 GCCCATTTTTATCUACTTCCATCTTGUCA F91 98 TGTAAAGAGACAGCCUTTCCTCUGA R91 194 AGTTCACAAAUCCATCAATGTTGCUC F92 99 ACACUCTUGAGGGCCACAAAG R92 195 TGTGATTGUAGGGTCTCCCTUGAT F93 100 CCGCTCCUTGTAGCCAAUGA R93 196 GGGTCUGACGGGTAGAGUGT F94 101 CCACUTUGGAACAGGACCAAC R94 197 TCAAAGTCGTCAUCCTTCAGTTCUC F95 102 CTTTCTTCCACCUTTCTCCAGCUA R95 198 CATCGCTGUAGAACGCACCAUA F96 103 TCAAGCCCUCCAACATCCUAGT R96 199 GGAAACTTCTGTUCATACCGACATGUAG

TABLE B Primer SEQ Primer Sequence Primer SEQ Primer Sequence Name ID (target seq of Primer A) Name ID (target seq of Primer B/C/D/E) F97 200 GAGGTCGTATUCGTCCACAAAAUGGT R97 469 GAGGCAGGAGACCCUGUAGGAG F98 201 GAAACTGCTTAGUAACTAGCAGAAGTGTUC R98 470 GAGGATAUATGCCAUACCCCAGCAAA F99 202 GACAAAGTTGUGTGTTGTAAGUGGAACA R99 471 GACCAAGAAAGGCUTGTGTCTACATTTUT F100 203 GAGCACCAATCUTTCTTCTGCCTTTUG R100 472 GACCAAAUCAAGAAACCTGTTUGAGAGAA F101 204 GAGGGAUCCCAAGGAAGAGAAGUGA R101 473 GACACTTCCCUTGTGGGAATGUCAA F102 205 GAGCTACTCTCCUGAACTCTCTCACUC R102 474 GATGCATCAGAACCCUCCTTGAAUC F103 206 GACTCCCAGUTGCAACGTUAGGT R103 475 GAGGUCCACGGAUCCAGAAACAAG F104 207 GATCACGUGTCCCCCTUCCA R104 476 GAGGTTCCTCCUCTCCTGGTCUC F105 208 GAACATTTGGCUGTGACTTCUAAGAAGAAA R105 477 GAGCTCACTAACUAACGTGAAAGCCTUAC F106 209 GAGATGAUCCAGATGTUAGGGCAGT R106 478 GAGGTTTTGCACAAGUTAGGTTTGTTTUG F107 210 GAGCCCAAATUGATTTCGATGATCTUCA R107 479 GAACCTTTATATCGTUACTCTGAATCTTATCTUCC F108 211 GAGCTCAAGAGUGAGCCACTUCT R108 480 GATGACTCTGTCUCCTCTTGTCTTCUC F109 212 GAATTAACACACAUCAGTGGAACTTCUGT R109 481 GAAAACGTTTTUCACCTTAGCATTTUGT F110 213 GAGCAAUCCAAAAGAAUAGCAGCCAAA R110 482 GACACCATCUCCATATCATUGAGACCAAAT F111 214 GACTTTGTGGAAUAGCCCATGAAGAGUA R111 483 GACGACAGACUACTTTGGTTCTCTTTUGT F112 215 GAACAGGAAGAGCACAGUCACTTUG R112 484 GACTCACUGACAAGCTCCUCGT F113 216 GACCATGCAGAGUGAAAGGATAUCCC R113 485 GAGCCTTTTCTTUTGCTTCCCTTGUT F114 217 GATGGAGCCGCUGACACCUA R114 486 GACAGGACCUGGCCCUGAC F115 218 GAGGTGUCTAGCCCAUGGGAGAA R115 487 GACCCAUCACACACCATAACUCCAC F116 219 GAGTCTGGUCCACATTGCTCUCA R116 488 GAGCTGUCCCCTCACCATUCAG F117 220 GAGCAAGAGUACACACTCCTCATTUGG R117 489 GATCACAACCCACUGAGGTATATGTAUAGG F118 221 GACTGGTTTCUGGTGGGACCATUA R118 490 GACAUGCACCGGAAAAGCGAUG F119 222 GACTCCCAGGCACUTGATGATACUC R119 491 GACATTTCTAGGUTACAGGCCUGGAT F120 223 GAGGGCTUGGTAACGTCCUGT R120 492 GACTCCAUGCCCCTCACUCA F121 224 GATGTGTCAAGGAGUTCGAAGATUCAC R121 493 GAATTGAAAATCUTCCTGCCTUCCCT F122 225 GAGUACAGCCAGTGTGUCCGA R122 494 GAGCAAAAGTGGUCCTCTCTGAAUCT F123 226 GACCATCCGGGCUTTACGCAAAUA R123 495 GAATATCAUCCAGCCTGTGTCTTUCC F124 227 GACCCCACUGAACCTCTCTTACATUT R124 496 GAGAGGGAAGGCAGGAUCTCUAAC F125 228 GACCCUAACAGCCATGCTTTCUC R125 497 GACCAGGCAAUGGAAAGGGTACAUA F126 229 GACGGCGAUGCTGAGAACCAAUA R126 498 GAGAAUAAAGAGGAGCAGGTUGAGGAA F127 230 GACCGACGUTGACCGCAUC R127 499 GAGGGCAAAUGAGCCTCUCAGT F128 231 GAAAATATTUCAGTGTCCGTUCACACACAA R128 500 GATCCAGATTGAUCTTGGGAGTGUAAAAA F129 232 GACCACACUGACGTGCCTCUC R129 501 GAGTCTTTGTGUTCCCGGACAUAGT F130 233 GAGCGCCACAGAGAAGUTGTUGA R130 502 GAGGGTCUGACGGGTAGAGUGT F131 234 GACCACAAAAUGGATCCAGACAACUGT R131 503 GAGCTTGCTCTGAUAGGAAAATGAGATCUA F132 235 GAACTGTTTCGTAUTTATAGCTGATTTGAUGGA R132 504 GACCTCTTCCUCAGGATTGCCTUT F133 236 GACCTCAUTGCCCUCAACACAGT R133 505 GATCAGTCCGGTUTTATTTGCATCATAGUT F134 237 GACACCACGUACCAGATGGAUGT R134 506 GACCCAAAGACUCTCCAAGATGGGAUA F135 238 GAAGACATGCAUGAACATTTTTCUCCAC R135 507 GATCCAGACCAGGGUGTTGTTTUC F136 239 GATGUGGAGCCTCTUACACCCA R136 508 GAGTGCCAGGGACCUTACCTTAUAC F137 240 GAACGTCTTCCUTCTCTCTCTGUCA R137 509 GACTGAGGUTCAGAGCCAUGGA F138 241 GAGAATGTGAAAAUTCCAGTGGCCAUC R138 510 GAGUCATATCUCCCCAAACCCCAAT F139 242 GAGGGTGTGUGGTCTCCCAUAC R139 511 GAGCCATAGGGCAUAAGCTGTGUC F140 243 GAGGATGAGCUACCTGGAGGAUGT R140 512 GACCTTGGTCCUTCACCTAACCTUG F141 244 GAGGTCACTGUACACCTTACACAUGAA R141 513 GACCCTCUTTAGCCAUGGCAAGG F142 245 GACATCACUGTAAACCTUGCAGACAAAC R142 514 GATGGTCTCUCATTCTCCCAUCCC F143 246 GAGCTTCTTGGUCGTGTTCTTCAUT R143 515 GACTCCTCCUGTGATCTGCAAUCT F144 247 GAUGGAAGCCCAGCCATTUCTAAA R144 516 GAGATGAUGAAGATGATUGGGAAACACAAG F145 248 GAGCCCCUGAGCGTCAUCT R145 517 GAGGGCTGUGCGTCACTGUA F146 249 GAGAGCTGGUGGAGGCUGA R146 518 GAGGAGCCCAGGCCUTTCUT F147 250 GAGUGACCGAGGACAACGUGAT R147 519 GAGCGTCCUACTGGCAUGACC F148 251 GACTCUGGGAGATCTUCACGCT R148 520 GACCACUCACAGGTCGTGUGT F149 252 GAGGATTGCAGAUTGGGCCTUG R149 521 GAACATGATGGAUGTCACGTTCUCAAA F150 253 GAATAATCCAUTGCCTGTCUAAAGAACACT R150 522 GATGTTAACCUTGCAGAATGGUCGAT F151 254 GAGACTTGGUGTTGTTGAUGGCAAA R151 523 GACUGCAGGATTCCUACCGGAA F152 255 GACCAACAUGACTTACTTGAUCCCCAT R152 524 GAATCACCAAAUGGCACCAUACGA F153 256 GAACCCUGGCCTACCTGGUC R153 525 GAAGTTCAAGCUGAAGAAGATGUGGAA F154 257 GATGAAGCAGCAAGUATGAUGAGCAA R154 526 GACTGACACCUAGCTGTGATCCUG F155 258 GAGGCACGGTUGAATGTAAGGCTUA R155 527 GAACTGATATGGUAGACAGAGCCUAAACAT F156 259 GACCACACCCUGTTCACTCCTUT R156 528 GAGTCTCAGTCAUTAGAGCACTCUGG F157 260 GAAAGGTGATCUATTTTTCCCTTTCUCC R157 529 GATTTCATACUGACCAAAACUCAGCCT F158 261 GAGCTTTTTGCUAAAATGCATGTTUCCAA R158 530 GAGACACGGCUTTACCTCCAAUG F159 262 GACAAAGAATGGUCCTGCACCAGTAAUAT R159 531 GAAGGCCTGCUGAAAATGACTGAATAUAA F160 263 GATCCTCATGUACTGGTCCCTCAUT R160 532 GAGTAAAAGGUGCACTGTAATAAUCCAGACT F161 264 GACAGATCTGTATUTATTTCAGTGTTACTUACCT R161 533 GAGACTCTGAAGAUGTACCTATGGTCCUA F162 265 GACATGTCAACAUCGCTCTAATUCAGAGA R162 534 GAGCTTTUCAAAAGGCTUAAACACAGGAT F163 266 GATGTTACGCAGUGCTAACCAAGUT R163 535 GAGCAAACCACAAAAGUATACTCCAUGGT F164 267 GAGCTGAUTTTGGTCTUGCCAGAG R164 536 GATCTGACTTGGUGGTAAACTTTTGAGUT F165 268 GACCTCACCTCUATGGTGGGATCAUAT R165 537 GAGTTCTTGCUGGTGTGAAATGACUG F166 269 GATTCGCCTGUCCTCATGTATUGG R166 538 GACACCCCCAGGAUTCTUACAGAAAA F167 270 GAGCACUGGGACTTTGGTAATUCAC R167 539 GACATCTCTUGGAAACTCCCATCTUGA F168 271 GACAGTGAAAAACAAGCUCTCATGTCUG R168 540 GACCACATGUGTCCAGTGAAAAUCCT F169 272 GACAGTGTGUCCACCGTGAUCT R169 541 GAAGTGAAGGAGGAUGAGCCUGA F170 273 GATGGAATGCCAGAACUACAATCTTTUGAT R170 542 GAGTGGAAGATCCAAUCCATTTTTGTTGUC F171 274 GAGACGCAUTTCCACAGCUACAC R171 543 GAAGCATCAGCAUTTGACTTTACCTTAUCA F172 275 GAGCTTTGAAUCTTTGGCCAGUACCT R172 544 GACATAAGAGAGAAGGUTTGACTGCCAUA F173 276 GAGATGCAGCCAUTGACCTGTTUAC R173 545 GAAGAAAACCATUACTTGTCCATCGUCT F174 277 GAGGGATUAAAGCTGGCTAUGGCA R174 546 GACCTTGTUGGGACCTCAGAUGT F175 278 GAAGCAUACGCAGCCTGUACC R175 547 GAGTGGUAGCAGTGGAUGCAGAA F176 279 GAGCTUCCAGGAGCGATCGTUT R176 548 GAAGGCCCCAUACAATTTGAUGACA F177 280 GAAGCTCGTUCATCGGGACTUG R177 549 GACCATGGUGCACCUGGGAT F178 281 GACTGGTUACTGAAAGCUCAGGGAT R178 550 GAACTTTGCGUGGTGTAGATATGAUCAA F179 282 GAGGACTCTGUGAGTGGGATTTGTTUT R179 551 GAGTCTTCACUCACCTCGGAUGA F180 283 GACATCCCUGACTGTGAGAUCAAGAA R180 552 GACAGGUACGCCTCCAGAUGAG F181 284 GAATCAACCUGCTTGGTGTCUG R181 553 GAAACUCCCGCAGGTTUCCCT F182 285 GAACGAGGACCUGTGGGACUC R182 554 GAGTGCCTUGCCCTTTTTGUGG F183 286 GACATUCCCCAACAGCTGUGGT R183 555 GACCGGGAUGCCAGGAUACG F184 287 GACCTTCCUCCTGAAGGCCUGA R184 556 GAGGGCUGTACCTCCUCAGAGA F185 288 GAAAGTGCUTGTGCCCUGCAT R185 557 GAACAGGCUGCCCAAGGGCUA F186 289 GACCCCTCTUGGACCTTAGAUGC R186 558 GACAGUGATCAGAUGAGCAGCAG F187 290 GACGCAUGGAGAAGAAACTGCAUG R187 559 GAACGGUCTUGGAACCCAGAGA F188 291 GATCCCCTAUGTGCAAGTCCUAAAG R188 560 GAGCTATTGAUGTCTGCAGTCUGG F189 292 GACCACTGUGCAGAAGCTCUCC R189 561 GATUGACTUGCCGGAAGAGCCT F190 293 GACGCCGGCCUCGTGAGUC R190 562 GAAGACCUCCGAGTCACTCCUG F191 294 GACAAATGCUGAAAGCTGTACCAUACC R191 563 GAAAAAGACTCGGAUGATGTACCTAUGG F192 295 GATGAGGCAGUCTTTACTCACCUG R192 564 GATTCCTTTCTUCCCAGAGACATUGC F193 296 GAGCAAAGACUGGTTCTCACUCACC R193 565 GAACATCCCUCTCTGCTCUGCA F194 297 GACGAUCTGTTCUACACGGAACCC R194 566 GAGGCTGGTTAUTGAAACCTTGTTTUACAT F195 298 GACCAGACAAGCCUACAGTAGGAAUC R195 567 GACTACCCCCGUACCAAGUACAAAC F196 299 GACTCCACAGACCCUCTCCTUGC R196 568 GATCGUCGAAGCGGCUGAC F197 300 GAAGGGTGTCUCTCTGTGGCTTUA R197 569 GAGACTCTGUAGGCTGCAGTTCUC F198 301 GAGTTTCUGCAGATTGACTUGCACA R198 570 GACTTCTTCCUACCTGTTTCCCAUGAC F199 302 GATCAGGAAACAAAAAUTTGTGCTAUGCAA R199 571 GAGGACCCAUTAGAACCAACUCCAT F200 303 GAGCTGGAGGAGCUAGAGCTUGAT R200 572 GAGGCTTGUGGGAGACCTUGAAC F201 304 GAGGGCTGUCGTGGTAGACTUAGA R201 573 GACCTGGTAGTCUCAAGCAGATGTTAAUG F202 305 GAAAGACTTCUCAAATTGTTGCCATTUCAG R202 574 GAAACGGACATGAGUTTGTTTTCCTTCUA F203 306 GACGAGGAAGAAAAACAAUCCCACTUG R203 575 GACAGCCAACAAGAUTCTGAAGAACAUG F204 307 GAGAGATCCTTUCGAAGTCATCGTCUT R204 576 GATCCCTAGGUAGCTAACCCCUAC F205 308 GAGGGCAAUGTCAATTAGCUGGAAC R205 577 GAAAAACACGGCAUGTGAACATTCUG F206 309 GACACTGTGTTACUGCCATCGACTUAC R206 578 GAGTATTCAUCGAGATTUAGCAGCCAGA F207 310 GACTTTTACCCUCTTCAGCTCAGTTUCT R207 579 GAGAGAGAGGACUGACTATCGGACUG F208 311 GATCTCCTCCAACCUAATAGTGTATUCACA R208 580 GAGACTGUCAAGCAGAGAATGGGUAC F209 312 GATTTCGUAAGTGTTACUCAAGAAGCAGAA R209 581 GAGAATAGGATATTGUATCATACCAATTTCUCGAT F210 313 GAATGCCCCCAAGAAUCCTAGUAGAA R210 582 GAACGAAAATGUAAGAAGATTCATCTUGAAGAAG F211 314 GAAGAGATGATTGUTGAATTTTCCTTTUGGG R211 583 GAAAAGCCATTTTUCCAGATACTAGAGUGT F212 315 GACGGAACUCGAATCGCUACCCT R212 584 GAGGGUCCCCAAGACACCUACG F213 316 GACTCGATGCUGTTCCCAGGUAC R213 585 GACCGAGAACUGAGGGTGGUACA F214 317 GATCATACAGACACUTCATTTGGAGUACC R214 586 GATACTAGAACUCAAAACACTGGCTGUT F215 318 GAAAAAATAAAGCTUGGCTTCAAGTTGUCT R215 587 GAGTAAGTCTTCACUTTCAGATTTTAGTUGGG F216 319 GAACATTGTGACCUTAATTTTGTGATCTCTUG R216 588 GATGCTTCCTGGUCTTTAGGATTTCUT F217 320 GACCCCACTCAUGTTTAGCAGATGUA R217 589 GATTTTACTTCUGCTTGGTGGCAUG F218 321 GAGGACAGGUTTTGTTGTUGAGGAAG R218 590 GATTTTACCCTCAUGGCTTAGTAGCATTATUT F219 322 GAAGCAAGGTCAUAAATTATTCTCCATATTTUCCA R219 591 GAAAAAATATUCATCCAGCTUCAGGAAAAGG F220 323 GATCTTTTTACCTUATAGATGGGAAACAUGAGAG R220 592 GAATCAGTCUGGTGGATGGGUAACA F221 324 GAATGTGTCTTTCAUGAGAAAAACAAGATCAUT R221 593 GACTAATAATGAATAAUTGGGTATGAGGCUACAGT F222 325 GATAGTAGCTGAUCCACAGAAGTTCAGUA R222 594 GATGTGAGAGAGCAAUCAAGGAGUG F223 326 GAAAGACTCTGAAUACCACCATCAAGAATAAUAAA R223 595 GAGTCTGAGAGUAGAAGGCAGATTCTGUA F224 327 GAATCTACAGGCCAAUGGTTCCTUC R224 596 GAAACTTUGCGGAGATCUGAAAACCA F225 328 GAGCCAGTAGUCACAAAGATTTCTUACCA R225 597 GACTCTAAAGAAGGAAGUGAGAACTTCUCC F226 329 GAAGAAGAUTGGGUGGGCAGAC R226 598 GACTTTCTTCACUCAAAGTGCCTATTTUGAC F227 330 GAAACCACTGATACAUTTTTCTACTTTCCUGAA R227 599 GATTCTTTTGAGAACUGAGTGATTTAUGACCT F228 331 GAAGACTTCTTUGAGATATTTCCATAGCUCAC R228 600 GAAGAAGTUAGAAACAGAACTGTATGUAAGCAT F229 332 GACATTTTTGTTTATGUTATTCTCTCTACCUCAGC R229 601 GAGCTATACGAACTUAGAAGTGAGAAATAATCUT F230 333 GAAGTTATAGGTAAUCGATGCATATAGCTCAUCT R230 602 GATTTCTCCAGGUCCAAAATGAATAACTATTUGA F231 334 GAAATTGTTTGTAGGGUTGGTTATTAGTGACUAT R231 603 GAATCCAGGAUAGGAAGCACACAUG F232 335 GACCACTATGUAAGACAAAGGCUGGT R232 604 GATTTTATAACTAGATUTTCCTTCTCTCCATUCC F233 336 GAGTTTCTGUAGCCCATACTTTGGAUGA R233 605 GAAATTCATACAUTTTTCTCTAACUGCAAACAT F234 337 GACACTGUGAAGGCCCTTTCTTCUG R234 606 GAGCAGTTGUGAGATTATCTTTTCAUGGC F235 338 GAGCATAGGAGATAAUCATAGGAATCCCAAAUT R235 607 GATGTTTTTCTAAUGTGTTAAAGTTCATUGGAAC F236 339 GAAGTCACTGGAAUTGTTGGGCUAC R236 608 GACCATGACTGUCACAGTGACCUT F237 340 GACTUCCAGGAGCCGUAGAGTTT R237 609 GATTGUGGCCCAAACAAAGCUC F238 341 GAACTCTTCCTATTUTTGTAGTGACCTGTUT R238 610 GAGTGCTTGGAAAUGGAATGGTTTUAGAAT F239 342 GATTCCTGAUAAAGCACAGCTGTAGUG R239 611 GACTACTGUAACCAAGAGGTGACTUCAG F240 343 GATTGTUCAAGCAGCGAGUCC R240 612 GAAGCCGAUATCCCUGCAGAC F241 344 GACATGAACUACCTGGACCGCUT R241 613 GAGTCGGUGTAGAUGCACAGCT F242 345 GAGGTGCTGUCTGGGAAGAUGT R242 614 GATGCCCAAGGUACTGCAUGGT F243 346 GAAAAGAGGCAGUAGCATCTTCUCC R243 615 GACUCACGCCUAAACCAGAACC F244 347 GAAATCCTGGAGCUTTGGTGTCTAATUC R244 616 GATAGCTGGCUCCGCACCUT F245 348 GATGCAGAAGCGGUTTCTGUG R245 617 GACTGCUGGGCGCCGUAAC F246 349 GAGCCTCAGAGAUAAAGGCAAAGATUG R246 618 GAACCCACACAAGCGAAUCTCUG F247 350 GAACCATTATTTCTTUGTTTTGTTTTTCCTGUAT R247 619 GAACTTTGCUGCCTTAATGACATUCC F248 351 GATACCAACCAAGUTTCATUAACCACAGT R248 620 GAGGTACCUGAGATGGAGGAGUC F249 352 GACCATGTTGGUCACTTACTCAAAGATTUT R249 621 GATTGAGCCACUAAGCAGTAACCATUC F250 353 GAAATGGGCAAGGUATGGATGUGG R250 622 GACCCGAAGUTCTTCTGCAGUCC F251 354 GATGGCGCAUCAGATCCTAGTUT R251 623 GAGCCGAAACGAUCAAGGUGAGT F252 355 GATGTAACAACCUAAAGGGAATAGGAAGAAUG R252 624 GATCAGTAGAAAGAUGGTACCAAAAUGGGT F253 356 GAGGCACTGGUTCTCATTCCUG R253 625 GAGACCGAGCUCGGGTGUAT F254 357 GAATGACTCAAUACCAACCCCUCCA R254 626 GAGCCTTTGTGGUCATGGGAAAGTAUA F255 358 GACATAACCATGAUATTAATAGGACTCCUGCT R255 627 GAATTTGCCTGAAATUACACATAGAACTTTCUG F256 359 GATGAACGCAAAACCUGTTGAAGTUAAAA R256 628 GAGGGATGGGUGACTGAGAUGGT F257 360 GACTTAAAAATGTCAAUATCTGGCCTCAAAUACG R257 629 GAGTGGACAUGCGAAUGGAGGA F258 361 GAGGGAAGCAATUTGCTACACTTTAATTUAAAC R258 630 GATTTACTCTGACAGCUAAATGAACTCAAATGUA F259 362 GAACAGAAGCUTCTAATCCUCAACGT R259 631 GAAGGCTCAGAACACUTTACTGAATTTUG F260 363 GAAGTTGAUGCCAATTCACAAUCACCA R260 632 GATTACTTAGAAGAAAAUTGCTCCTTGUCAGA F261 364 GACTGAGGTCTATUCACTTTCTTTTCATCTTUG R261 633 GAGTGAAGGAAACCAUTCGTGAUAAAGC F262 365 GACTATTTGTTTCTUCCCCATGGAATTGUC R262 634 GAGAAAATUGGACCCAGTTCTCUGCT F263 366 GATAATCTTUGAACTGCCTGUGCACT R263 635 GAATCTTTCAACUGTAAAATTCACTGUGGGT F264 367 GAAAGCAAUGGCTTGGGAAGUAAGA R264 636 GACCATTCTCAUATCCTAGGTCUGCCT F265 368 GATCTAAAGGTTTTTCUGATTTCCTCATTAGGAUT R265 637 GAGCACUCCATTTUGGACAGCAA F266 369 GATCCAGTCATTTUGAGAAAGACAACTUACT R266 638 GAGTTTATTTTCTGGUTTCAATAGAACAAGTUGA F267 370 GATTCATTAATATTTUCAGATCACCAGTTGATUG R267 639 GATTTGAAAGGTAGAUTGCCATAATGTATCATUG F268 371 GAATTAACTGTACCUCCAACTTTCTTACTATAUGC R268 640 GAATGTGGAATCTUTGTTTAGTTTTACTCUGGT F269 372 GATTAAGAAACUAGAAACTGTTTAGACUGCCT R269 641 GAATGGTTTAGTCUGACACATATTTAACACUT F270 373 GATGGTTCTGUCGACTAAACUGC R270 642 GATTTTCAAGTTAUAGAAACATGTCATGTTGUCA F271 374 GAACGGACACUATGTCCTTAAGCUGA R271 643 GACTAGACTTUGAGACCTGCTAAATAATUAGATG F272 375 GATTGGCAUGGCTTCTCUAGCT R272 644 GACAGGUCCAAGUGAACCAGGGA F273 376 GACACCTTCUACCGCTCACUGC R273 645 GAAGGGCACUGACCCTGGUA F274 377 GAATTGACUCTGAATGUCGGCCAA R274 646 GATCTGCAGGAGGGUGCTCTUA F275 378 GACTCTGCCCCUAAGAAACCUGGA R275 647 GAGGGCAACUACACCTGCATUGT F276 379 GAATTACTCUAACTTTCGCAUGCACAC R276 648 GATGCCAAGACAGUGAAGTTCAAAUG F277 380 GAAGUGGGCAGCAGTTTCUGA R277 649 GAGACACCACCUACTTCTCCGUCA F278 381 GAAACCAACTGCUTGTATGCTTTCUGG R278 650 GAAAGACCAAAAGAGAAUGGAAAGTACUGAC F279 382 GAGCAGCCUTACCTGGTUGGA R279 651 GAAGAGUATCCATCUCCAGGAGACG F280 383 GATTACAGCUCGTTGGUGCAGT R280 652 GATGTGGCUCTCCGCCCAUT F281 384 GAATGGAAACCCUGACAGAGTCTTUG R281 653 GAGCTACACCATUAGCTTCACTGATTUT F282 385 GATGTTATGAGCUTAGCACCTUGCAG R282 654 GACTGGATGGUAAGAGGAGTTTCTTCAUC F283 386 GACCAGTTCUGCAGTTAGAGGTUG R283 655 GACCTTTCCCCUCCCCTACCUAG F284 387 GATTTGATTCTTAAUCACCTAAGGAUGGCT R284 656 GACAAAACAAAGUCAAAGAGAATTATGAAATGUG F285 388 GAATCCGTACCUTCCACCAATCUG R285 657 GACAGGGATTTUGGTTACTACTTTGCUAAGA F286 389 GATATAACAATGAAUGACCAAAAGGAAATUAACAA R286 658 GATTGTCTTCUGGACACGTTCUGAAA F287 390 GATAACTTTCCATAUGCAAACCTACTGGCUA R287 659 GATATTAAGCTTTCUTGGAAAATTCTCTTUCCCT F288 391 GACCUGGACGTCTUGGAAAAGGG R288 660 GATTCAGAAGTUAGGAAAGGAGUCCAG F289 392 GATCTGGGUCAAGGAUGGCACA R289 661 GACACCUGUCACCCGCACAC F290 393 GAGCCCACUTCCCATCUGGGT R290 662 GACAGTCAGUAACGCCAGUGAGT F291 394 GATCCCCGCUGCTGUGCAAC R291 663 GAGUCCCGTGGUGCAAAGGC F292 395 GACCCACATGUCCAGCACCUT R292 664 GAATGTACACTAGTTUCCGGAATAAACCTTUT F293 396 GAGCTGGUGAAACAGGTAGUGAGT R293 665 GACTUGACCCCUGCGAGCCA F294 397 GACTCCAGGUCCTTGTGUGAGC R294 666 GACCCACUCAAGCTCAGCTGUAA F295 398 GACCTCACGAACUGTGCTGAUGG R295 667 GACTGAGAATGGCUACCTCTCGATAUG F296 399 GAGGATTCGAGAAGUGACAGGCTAUG R296 668 GAGGCTGGAGUTGGTGTTATAGTUCAA F297 400 GAATTGGTAGCUGGTGATGTTCCUC R297 669 GACTCACACATCUTGAGCCCATTTTTAUC F298 401 GACAGCTAATUCATCTGGAGAUCAAACCC R298 670 GACTGAGAGGGUGTCACATACCAUG F299 402 GATGTCAGTTCCCUCCTTTTCTATTTTCUC R299 671 GATTCATACCGACAUGTAGGACCTUGT F300 403 GATGGGCACGGUAATGCUGCT R300 672 GAACTTCUCACACCGCTGTGUT F301 404 GACTCUGCGGTGGTUGGCAT R301 673 GACCTCACCUCCGTTTCCUGCA F302 405 GACTCCACCUCCAGGAACTTACUC R302 674 GATCUGGCCCCCTUAGGAGGA F303 406 GAGGGATCTTGUGAAATGTCATCTGACUC R303 675 GATCATCCTCUCCCCATAGAAAAGUCC F304 407 GATCAACCCTGTUTTTCTCCCTCTTATUG R304 676 GATCTCUGCCATCATTUCCGGAAAG F305 408 GACTGUACAGCATGAAGUGCAAGAAC R305 677 GATGCAAGGAAUGCGATGAAGUAGA F306 409 GACCATTAACAUGGCCTACCAGAGUT R306 678 GAGTCGCUAACACGTGTGTGTUC F307 410 GATTGCCUAGACAGCACCGTAAUG R307 679 GATGGCTAAACTUGACCTTTTTACTCUGC F308 411 GAGACGCAGUTTCTTCTTCTCAUCG R308 680 GATTCCTCAGCAUCGACCTUGC F309 412 GATATCGAGTGTGUGCATATGTGTATGTUG R309 681 GAAATCTATATACTUCCTTACCTGGGATUGGA F310 413 GAAGGGAAAAUGACAAAGAACAGCUCA R310 682 GAACATGCTGAGAUCAGCCAAATUC F311 414 GAGGCCTGCUTTTGGAGTCCUAT R311 683 GAGCAGUGAAAAGAGTCUCAAACACAA F312 415 GAGAAGAGCCUCCACCATCUCCA R312 684 GACCCACAGGCCUTCTUCGAG F313 416 GACACACAUGCCATCATTCUAGGAAG R313 685 GACTGGUATGAGAAACUGCACGAGT F314 417 GAGAGGTTTUCCAGCACTCTGACAUAT R314 686 GAAATACCAATCUATTGTGGGCTCUGG F315 418 GATCTTCTCTGUTTCAGGGCAUGAAC R315 687 GACCTCCTTCUGCATGGTATTCTTUCT F316 419 GAAGATTCUGCCGAACCAATGGAUC R316 688 GAATTAAAGCAGUGCTCATGATUGGG F317 420 GATATGACTUGTCACAATGUCACCACAT R317 689 GACGGGACUCGAGTGATGATUGG F318 421 GAGTGCCCTATUACCTCAATCATCCUG R318 690 GACTTCACCTTUAACACCTCCAGUCC F319 422 GATCAGTTACTACCUGAAAATGACACTTUGT R319 691 GACTCCTCTAGCUATCTTAATGACTUGGAC F320 423 GATAAAGACCTUCTTCCGTGTGUCCT R320 692 GACTGCTTTCATUCATAGGGAAATACAUAAGAAA F321 424 GATACATTTATTTUGAGAAACTTGAGAGAACUTCA R321 693 GATTCAATATTTTAAAUAGTCTGGCCUAAACGGT F322 425 GAAGATGGTGATAGAUCTTTAAGAGAATTGCUT R322 694 GATGATTTCCAGUATTAATTGGCAAUAAGAGAAT F323 426 GAAGCTTTTGATAAGAGUTAGGAAATCACTAGUC R323 695 GAATGAAAGCUAAAACATAAGATGAAUGGGAAAA F324 427 GAAGGAUAAAAACCAGCATTATTTATTUGAGCA R324 696 GAATTATTTCTTACCACUTTTCCTTTCTCCUGT F325 428 GACTGACCCAUAATCTTGCACCATTUACC R325 697 GAATTGTGAGATUAACAGCAGGGAUACC F326 429 GATTTGAAATGAAUGTTCACGACAAAUGC R326 698 GAGCTTCATTGTCTUGATAAAATTTATGGTATCUT F327 430 GAACAACCAAAACAAUACACACAGAGATTUT R327 699 GACCAGCTCTTUCATATCTTAACATTUAGCAACA F328 431 GAACGGAGGGUCATGTGTATATTAAGUAAG R328 700 GAGCCAAAACATTTUGTCCCTTTCTATAATTUG F329 432 GAGAATTAAGUGTGTACTACUCCCAAGAGAAAA R329 701 GATGGACTTCAAGUGATCACTTGUG F330 433 GATATAGGATGAGUAGCTCCAAATTAATGAAUGT R330 702 GAAGCCTGUGGTGCTTTTUGCG F331 434 GAGCTGTAGAAUAGTCAAGAGGAATUGCA R331 703 GAAAGTCAAACUACACTCAGAACCUGAAT F332 435 GACTCAGTGCUCTAAATCCAGAGCUG R332 704 GAGCAAAGGCCAAAGAUAAAATGCTTACUG F333 436 GAATGAAATATUGTCAACTCTCTUAGGCAAAAT R333 705 GAAAGCTACAGAAUGTGAACAGTCTTCTUAAA F334 437 GATACTTUGCAAAGCTGAATUAGACAGCA R334 706 GAGAGGTAGAUGCTGTAATTGCTGAUACAA F335 438 GAACATGAGCAUCACATTTTCCTUGG R335 707 GACAAACACCTCCUGATAAATTGGCTTUG F336 439 GATGCCTTATGAAUATATTCACGCUGACT R336 708 GACCCTACUCCAAGGAGCUCAGG F337 440 GAACCAGGUAAGCACCGAAGUC R337 709 GACCCAGTUACCATAACTACTCUGAGAAAA F338 441 GAACCAAGCCGCUGGTUCA R338 710 GACTTGCAGAGCUATCCCCUAAAGC F339 442 GAAGACCCCUTTAACTCAAGACUGC R339 711 GAGCTGCACCGAGUCGTAGUC F340 443 GAGCGAGGAUATCTGGAAGAAATUCGA R340 712 GAGTCGUTGTCUCCCCGAAGG F341 444 GAUTCUCCACGGCCGACCA R341 713 GAATACAGTCCUGGATGATGATGTTTTUGA F342 445 GAAAGTCCCUCAAAAATAGGAGGUGCT R342 714 GAGGACAAGAAAAGUGCAACTUCCCA F343 446 GAGACAGAUCAGCAACAACCGAAAAUG R343 715 GATTTCATTGUTTTCCAACUCCGGGAT F344 447 GATTTGTCCAGAGACCUTTCTAACGTAUT R344 716 GATTUCCACAGAAACAACAUCGATTTCTTC F345 448 GATTTCUGAAGAGGACTTGTUGCG R345 717 GATGCATTUGATCATGCATTUGAAACAAGT F346 449 GAGATTTTUCAGTTAATAATAUCCCCCGAGCT R346 718 GAAGTCTGUGCGCGCTUGC F347 450 GAAATCGCCUCCGGAUCCC R347 719 GAGTGCGCACGUCGCAAUC F348 451 GAGTCATTCCTTCUTTTTAAAATGGTGCTUAAGT R348 720 GAGGATGTAUACAAAAGGCGGATGUG F349 452 GAGGTCCCCCACCUCTCTTTUG R349 721 GAGCCAGAGAGUCCCTTUCACC F350 453 GACTCUCCAGGAAGGCTCACAUC R350 722 GATGCCACTCUTTGGGTTGAGUT F351 454 GATGGCATUGCCTTGTCCTUG R351 723 GATTTCAAACUGGAGGCTTAUCACCAA F352 455 GAGGCAGAAAACCAAAACAUTGGCTUA R352 724 GAATACAAGCATGAAAAUCAAAACATATCTTCUGC F353 456 GAAATTGTTCCTCAAGUTTGTTTAAGGACTUAAAA R353 725 GAGTAAATGGTAGCTUTTATCATAATCACCAGUC F354 457 GAAGTGGTATCAUCCCCATTTAATAGCUG R354 726 GATCCATTCAAGACUTTAGCAGGTGGUA F355 458 GAACAAATACAAAACUGTCCACATCTATGTUG R355 727 GAGTTACTCTCATGUGAGAACCATTTGAAUGA F356 459 GAAACAAACCATAGCUATAATGAAGAACTTGCUA R356 728 GAGTTTTTCTTATCUCTTAAAATGTTTCTGCUACA F257 460 GAAATAGTTGATCAUACTTTGTAACAGAAUCACA R257 729 GAAAGGUACAAGTUAAGGCACACAGAAG F358 461 GACTCATCTCCCTUTAATTTTGGCACATTAUT R358 730 GATGGATCTUGGCACAATGAUAACAGG F359 462 GAAACTATCTUCTTTGGACTTCUGAAGAGAC R359 731 GATGCTATAGTACCAGUACCTTTTAAGGTUCA F360 463 GAAGTAAATAATGGTTUCTCCTTCTCTTACTTUG R360 732 GACCGTAAGGUGGCCTACTTUGC F361 464 GATTCCTGGUGGCATTCAAUAAAGCA R361 733 GACAGCGTTTTCUTGTATTCCTGTATTUAGC F362 465 GAAGGAGCAACUTAGGGATCUGGT R362 734 GAGGAACTGTGAAUGAACTTGTAGGUG F363 466 GAACCCCTAAUCTGGTCAACCUG R363 735 GACCUGACCAGGGCGUCAAA F364 467 GAAGAAATAGAAAACUACAGGACGTTAUCCAG R364 736 GAAGTTCATCTUCGAAGCTCAAATTUCAG F365 468 GATCCGCTTTCUAAAATGTCAGTTGUC R365 737 GATACAACAAAAUGTTTGACTTCAUGCAGGT

TABLE C Primer SEQ Primer Name ID Primer Sequence Name SEQ ID Primer Sequence F366 738 AAAACTCAGTAUCAACAACTACCGGUAC R366 870 TCCCGTGGCUGGTAAATCTGAAAUA F367 739 CTCAGAAAUGGAAAAAACCTGCAGUAAA R367 871 CCAAAACATGAAUGTTCTCAACAAGUG F368 740 GTTCCCTCUGCGTGTTCTCAUAA R368 872 ATTCCTGCACUAATGTGTTCATUCT F369 741 AAGAACCTGUGTGAAAGTATCUAGCAC R369 873 GUCCAAAGCGAGCAAGAGAAUCC F370 742 AUAAACCAAACCCAUGCAAAAGGAC R370 874 AGTTCCAGUAGTCCTACTTUGACACT F371 743 GCATTGAUGGAAGGAAGCAAAUACA R371 875 AGAGCACGTUCTTCTGCTGTAUG F372 744 CCAGCTTCAUAGACAAAGGTTCUCT R372 876 AGTTGAATATCTGTTUTTCAACAAGTACATTUT F373 745 GTGGTTTCTUCCATTGACCACAUC R373 877 GCCTGGCCUGAATGCCTUAAA F374 746 CAAAUGGGCAGGACTCTUAGGT R374 878 CAATTTCAACACAAGCUAAACTAGUAGGAT F375 747 GUGAGGAAACTUCTGCAGAGGT R375 879 TCAACAAAAGUGCCAGTAGUCATTTC F376 748 GGAAGCAGGGAAGCUCTTCAUC R376 880 CTGTTTTUAGCAAAAGCGUCCAGA F377 749 TGGTTUGAAGAACTTTCTUCAGAAGCT R377 881 AGTCAGCCCUTGCTCTTUGAAT F378 750 AGGGAGACUGUGTGTAATATTTGCG R378 882 TTGGCCAUACAAAGTGAUAAAGGACTT F379 751 GCCAGTATUGAAGAATGTTGAAGAUCAAAA R379 883 TTTGCAGGGUGAAGAGCTAGUC F380 752 GCCAAAAGGAAGUCTGTTUCCAC R380 884 TGTACAAAUGGGACTAACAGGUGGA F381 753 CATGCCACACAUTCTCTTTTTACAUGT R381 885 AGCATACCAAGTCUACTGAATAAACACTUT F382 754 GTAGAGUGCTACACTGUCCAACA R382 886 CCTGGAGTCGAUTGATTAGAGCCUA F383 755 CTCTGAGAAAGAAUGAAATGGAGTUGGA R383 887 AATGTGTTATGUGGCTCCATTATUAGCT F384 756 AAACAAATTTUCCAGCGCTTCUGA R384 888 GCATTTTTACCUACGATATTCCTCCAAUG F385 757 AGCAATAAAAGTGUATAAATGCCTGTAUGC R385 889 ACCAGTAAAAAUAAAGAACCAGGAGUGG F386 758 TCAACAAGTTGACUAAATCTCGTACTTUCT R386 890 TTATAGAGGTTTUCTACTGTTGCUGCAT F387 759 CATTCTTACAUAAAGGACACTGUGAAGG R387 891 GCAGTTGTGAGAUTATCTTTTCAUGGC F388 760 CCCTTACAGAUGGAGTCTTTUGGC R388 892 CATCATTCACCCUTGGCACAGUAA F389 761 AAAGACCTTTUGGTAACTCAGACUCAG R389 893 AAAUATTTTCTAGGAATUGCGGGAGGA F390 762 ACATTCACUGAAAATUGTAAAGCCTATAATTG R390 894 CAGGUAAUCGGCTCTAAAGAAACATG F391 763 GGTTGTGCTTTTUAAATTTCAATTTTATTTTUGCT R391 895 CAGAGAGATUCGAGGCAGAGUG F392 764 GGATGUCACAACCGUGTGG R392 896 AGTAGUGGATTTUGCTTCTCTGATATAAACT F393 765 AGTGAAAACUAAAATGGAUCAAGCAGATG R393 897 GCTCTUAGCCAAAATATUAGCATAAAAATCAG F394 766 AAACTAGTTTTUGCCAGTTTTTUAAAATAACCT R394 898 AAAAAGCATUGTTTTTAATCAUACCTGACTT F395 767 TTTTTACCCCCAGUGGTATGUGG R395 899 GGTACAGAUTTGTAAATCUCAGGGCAA F396 768 GAAAACACAAAUCAAAGAGAAGCUGCA R396 900 GAGAUCACGGGUGACAGAGC F397 769 ATATTTAGUAGCCAGGACAGUAGAAGGA R397 901 ACCTACCTGAUACCCCAGAUCCC F398 770 AAATATTTCAGUGTCCGTUCACACACAA R398 902 TCCAGATTGAUCTTGGGAGTGUAAAAA F399 771 GCAGAUGCAAGGTATTCTGUAAAGG R399 903 GTGTGCTAGAGGUAACTCATGATAAUGG F400 772 ACCTACATAAAACUCTTTCCAGAATGTUGT R400 904 GAAAGGGUCAACAAAAGAATGUCCAT F401 773 CCCTTTCTGTUGAAGCTGTCAATUC R401 905 GAAAGTTCCCCAAUTGAAAGTUGCAG F402 774 AGAUGGTATGTUGCCAACACGAG R402 906 AACTTTGTAATUCAACATTCATCGTTGUGT F403 775 GATGTTTCCGUCAAATCGTGUGG R403 907 TAGATGATAGGUGGTACATGCACAGUT F404 776 GTAGAACTATCUGCAGACACCUCAAAC R404 908 ACCUGAATTATCACTAUCAGAACAAAGCA F405 777 CCAGAACCACCAUCTTTCAGTAATTUG R405 909 GAACAGUACCCGTTCCCTUGA F406 778 ATCATAAAATGTUGGAGCTAGGTCCUT R406 910 CTTGAGGACCUGCGAAAUCCAG F407 779 TATGATGGAAGGGUAGCTGTUAGAAGG R407 911 TGGAAAGCTTCUCAAAGTATTTCATTTUCT F408 780 GGTTAAAATGTCACUCTGAGAGGAUAGC R408 912 GCAGCGTTTAUAGTCTGCTTTTACAUC F409 781 GGAAATTTGUAAAATGTGCUCCCCAAA R409 913 AACGGGCTUGGAAGAAAATAAUCAAG F410 782 AATTCCTTGTCACUCAGACCAACUC R410 914 TCTGCTAGCUTGTTTTCTUCACAGT F411 783 ACTAAGGTGAUGTTCCTGAGAUGC R411 915 AACAATATACCTUCTCAGTCTACUAGGCAT F412 784 ACTTTCCUTAATGTCATTTUCAGCAAAACT R412 916 CAGATAACTUAGAACAGCCTAUGGGAAG F413 785 CAGTCTGAACUACTTCTTCATATTCTUGCT R413 917 GGCCAAAATUGAATGCTATGCTUAGAT F414 786 CTAGTTCTGCUTGAATGTTTTCAUCACT R414 918 AGCACAATUAGCCGTAATAACATUAGAGAA F415 787 TGGAATGTTCTCAUTTCCCATTTCTCUT R415 919 TGGACTCATTACUCCAAATAAACAUGGA F416 788 GTTTCGTUGCCTCTGAACUGAGAT R416 920 GTCTAATATCAAGCCUGTACAGACAGUT F417 789 CCTTGATTTTCTUCCTTTTGTTCACATUCA R417 921 TGCAGAATACAUTCAAGGTTUCAAAGC F418 790 TTTCTATGCTUGTTTCCCGACUGT R418 922 AATAAATGTGUGAGTCAGTGUGCAG F419 791 GAUGAAAGCTCCTUCACCACAGAA R419 923 AAGCCTTCAUCCGGAGAGTGUA F420 792 CCTAGAGTGCUAACTTCCAGUAACG R420 924 TAATGCUGAAGACCCCAAAGATCUC F421 793 CTTGGAAGGCUAGGATTGACAAATUCT R421 925 GCCAAAUGAACAGACAAGUAAAAGACA F422 794 TTGTTACTCTTCUTGGCTCCAGTUG R422 926 GCAAATTGATAGUTGTTCTAGCAGUGAA F423 795 TTAGGTGGGCUTAGATTTCTACUGACT R423 927 CAGCAGTAUAAGCAATATGGAACUCGAA F424 796 TGCTTATAGGTUCAGCTTTCGTTTUG R424 928 GGAGCAGAATGGUCAAGTGATGAAUA F425 797 CCACTATGUAAGACAAAGGCUGGT R425 929 TTTTATAACTAGATTTUCCTTCTCTCCATUCC F426 798 TCCGTTTGGTUAGTTCCCTGATTTAUC R426 930 AGAGCGTCCCCUCACAAATAAAUT F427 799 GTATTATCTGUGGCTCAGTAACAAAUGC R427 931 GAAAGAGTTCACUCCAAATCAGUAGAGA F428 800 TTAAAGCCTCAUGAGGATCACUGG R428 932 GGTTCTGAUGACTCACATGAUGGG F429 801 AGTTCATCACTUCTGGAAAACCACUC R429 933 CCCTGTGUGAGAGAAAAGAATGGAAUAA F430 802 GGGATCAGCATUCAGATCTACCTTTUT R430 934 AGGCUGAATTCTGTAAUAAAAGCAAACA F431 803 TTCAGCCTTTTCUACATTCATTCTGUCT R431 935 AGGGTAGTTCUGTTTCAAACTUGCAT F432 804 TACCCTGAUACTTTTCTGGAUGCCT R432 936 TGTATATTTTCAGCUGCTTGTGAATTTUCT F433 805 GAATCCAAACUGATTTCATCCCUGGT R433 937 GACAGTTCTGCAUACATGTAACTAGUGT F434 806 AGCTGCCUACCACAAATACAAATTAUG R434 938 GCGGAUACAACCUCAAAAGACG F435 807 CAGAGTTCUCACAGTTCCAAGGTUAG R435 939 TGUCAAGTTTCTCTUCAGGAGGAAAAG F436 808 GAAGAAGAAGAAAACAAAUGGTTTUACCAAG R436 940 AAGGAAAATAACUCTCCTGAACATCUAAAAGA F437 809 ATCACCACGTCAUAGAAAGTAATTGUGC R437 941 TGTTGAAGAGCUATTGAAAATCATTTGUGC F438 810 CATTCAAACTTACTUGCAAAATATGTGGUC R438 942 ACAGCTCAAAGUTGAACTTATTCACUAAGA F439 811 GCATAGGAGATAAUCATAGGAATCCCAAAUT R439 943 ATGTTTTTCTAATGUGTTAAAGTTCATUGGA F440 812 AGTTGTAGTTGTUGAATTCAGTATCAUCCT R440 944 GCCAGTTTCCAUATGATCCATCTAUAGT F441 813 TGTGCCTTTCCUAAGGAATTTGCTAAUA R441 945 AGAAACCTTAACCAUACTGCCGTATAUG F442 814 AAAAGATAAUGGAAAGGGAUGACACAGC R442 946 GCCACTTTTUGGGTATCTGCACUA F443 815 CTGTTAAGGCCCAGUTAGATCCUC R443 947 TTCAAGAGGUGTACAGGCAUCAG F444 816 AGGCAGTTCUAGAAGAATGAAAACTCUT R444 948 GGTCAGGAAAGAAUCCAAGTTTGGTAUA F445 817 TGTACCTAGCAUTCTGCCTCAUAC R445 949 CCTCAGCTCCUAGACTTTCAGAAATAUG F446 818 TAGACCTTTTCCUCTGCCCTTAUCA R446 950 AAACTCCATCUCAAACAAACAAACAAATUAAT F447 819 CACATUATTACAGTGGAUGGAGAAGACA R447 951 CCTCCTGAATTTUAGTGAATAAGGCTUCT F448 820 CTTCTTTGGGUGTTTTATGCTTGGUT R448 952 GCAAAGCACGAACUTGCUGT F449 821 GCAGAGCTUTATGAAGCAGUGAAGA R449 953 GTGAUGGCCAGAGAGTCUAAAACAG F450 822 TCTTAAATGGUCACAGGGTTATTUCAGT R450 954 TGACATCCCTUGATAAACCTTGTUCC F451 823 TTCCATTGCATCUTTCTCATCTTTCUC R451 955 TTTTTGTCGCUGCTAACTGTATGTUA F452 824 TTCACTUCAGCAAATTTTTAGAUCCAGAC R452 956 GCTCCAACTAAUCATAAGAGATTTUAAAAGAC F453 825 TGCCCCTTUCGTCTATTTGUCAG R453 957 AAGTAAGAAGGCCUGATTTGGATUCT F454 826 GGAGATTTTTCTGUGTTTTCTGCTAGUC R454 958 GCTATTTCCTUGATACTGGACTGUCAAA F455 827 TGACAUACTTTGCAAUGAAGCAGAAAA R455 959 ATTCCTTGAGUTTACATTAACTUACCAGAAG F456 828 GGATCCTGATAUGTCTTGGTCAAGTUC R456 960 ATGACAATTATCAACCUCATCTGCTCUT F457 829 GGCACCAAAUACGAAACACCCAUA R457 961 TAAATTGUTTTTCTCCTGTUGAACCAGACA F458 830 ATATCTGTCAGTGAAUCCACTAGGACUG R458 962 CCTGCTTATTTUTCTCACATTCTUCCG F459 831 TGAAGAAGCAUCUGAAACTGTATTTCCT R459 963 GGTTUAGAGACTTTCUCAAAGGCTTAGAT F460 832 GGACTACTACTATAUGTGCATTGAGAGTTUT R460 964 GTGTTTUCACTGTCTGUCACAGAAG F461 833 TGGCTTATAAAATATUAATGTGCTTCTGTTUT R461 965 AAAACTATCTTCUTCAGAGGTATCUACAACT F462 834 GGTAAAAAUGCCTATTGGAUCCAAAGAG R462 966 GTGACGUACTGGGTTTTUAGCAAG F463 835 AATCTACAAAAAGUAAGAACUAGCAAGACT R463 967 GGCTTCTGATTUGCTACATTTGAAUCT F464 836 AAGTGACAAAATCUCCAAGGAAGTTGUA R464 968 AGGTCTTTTTCTGAAAUATTTTGGTCACAUG F465 837 GAATTCTTUGCCACGTATTTCUAGCC R465 969 AGATATTGCCUGCTTTACUGCAAGAA F466 838 GGCTTCTTCAUTTCAGGGTAUCAAAAA R466 970 TGTATTTCCAGUCCACTTUCAGAGG F467 839 AATACAUACTGTTTGCUCACAGAAGGAG R467 971 TTGTTTTCTTTTUCAAAGTGGATATUAAACCT F468 840 ACCGAAAGACCAAAAAUCAGAACTAATUAAC R468 972 CAGAAGGAATCGUCATCTATAAAACTATAUGT F469 841 TCACAGAAUGATTCUGAAGAACCAACT R469 973 CTGTAGTTTTTCCTUATTACATTTTGCTTCUT F470 842 ATTACCCCAGAAGCUGATTCTCUGT R470 974 TGGGATTGAAAGUCAGTATCACTGTAUT F471 843 TATATGATCATGAAAAUGCCAGCACUCT R471 975 GTTACCTTTGAGCUTGTCTGACATTTUG F472 844 TTCCCATGGAAAAGAAUCAAGATGTAUG R472 976 TTGGATTACTCTUAGATTTGTGTTTTGGTUG F473 845 ACTGTCAATCCAGACUCTGAAGAACUT R473 977 ATGGTAGAGTTCUTGAAAATGGGTUC F474 846 CAGGUGAUAAACAAGCAACCCAAGT R474 978 GTATTTTATCTATATUCAAGGAGATGTCCGAUT F475 847 TGGCATTAGAUAATCAAAAGAAACUGAGC R475 979 GCCTTTTGGCUAGGTGTTAAATTAUGG F476 848 GAATCAGGAAGUCAGTTTGAATTTACUCAG R476 980 GTCTACCUGACCAATCGAUGGG F477 849 GCCTGTUGAAAAATGACTGUAACAAAAG R477 981 AGCTTTTUGCAGAGCTTCAGUAGA F478 850 TGAAGATAACAAAUATACTGCUGCCAGT R478 982 GGCCAGATAATTUAAGACATATGTTGUGC F479 851 AGGAGGGAAACACUCAGATUAAAGAAGA R479 983 GCTCCGTTTUAGTAGCAGTTAACUGT F480 852 TTTCAGACTGCAAGUGGGAAAAATAUT R480 984 GTCTGTTTCCUCATAACTTAGAATGUCCAT F481 853 TCTTCTTACAACUCCCTATACATTCTCAUT R481 985 TCACTGTGCGAAGACUTTTATGTCUA F482 854 CCAGTTGGTACUGGAAATCAACTAGUG R482 986 TTTCACTTTGUCCAAAGATTCCTTUGC F483 855 AAAAGAGCAAGGUACTAGTGAAAUCACC R483 987 AGAATTCTGCAUTTCTTTACACTTUGGG F484 856 AAAAACCTTGTTUCTATTGAGACTGUGG R484 988 GGACTGATTUGTGTAACAAGTUGCAG F485 857 AATTCAGCCTUAGCTTTTTACACAAGUT R485 989 TCATACAAATAATUTCCTACATAATCUGCAGT F486 858 TGACAAAAAUCATCTCUCCGAAAAACAA R486 990 CAATACTGGCUCAATACCAGAAUCAAGT F487 859 AATAATTTTGAGGUAGGGCCACCUG R487 991 AACCTGCCAUAATTTTCGTTUGGC F488 860 TCATAACTCTCUAGATAATGATGAATGUAGCA R488 992 GAAGTTTCCAAACUAACATCACAAGGUG F489 861 GTATAGGGAAGCUTCATAAGTCAGTCUC R489 993 ATTTCAGAAAACACUTGTCTTGCGUT F490 862 AGAAGATAGUACCAAGCAAGTCTTTUCC R490 994 ACCACATTATAUGAAAAGCCTTTTUGGG F491 863 TAGTACAGCAAGUGGAAAGCAAGUT R491 995 GGUTTCTCTTAUCAACACGAGGAAGT F492 864 CAGGCTTCACCUAAAAACGTAAAAAUG R492 996 CTGTCAGTTCAUCATCTTCCAUAAAAGC F493 865 ATGAAATAUTTCTTTTUAGGAGAACCCTCAAT R493 997 TATACCAUACCTAUAGAGGGAGAACAGATAT F494 866 ATATATTUTCTCCCCATUGCAGCACAA R494 998 GCTTGAAGATTTUTCCAAAGTCAGAUGT F495 867 AGGACATCCAUTTTATCAAGTTTCUGCT R495 999 GTTTTGCTTTUGTCTGTTTTCCUCCAA F496 868 TGGCTCTGATGAUAGTAAAAATAAGATTAAUGA R496 1000 AGGCAAAAATTCAUCACACAAATTGUCA F497 869 GCTGTATACGUATGGCGTTTCUAAACAT R497 1001 TCATTGGAGGGUATGAGCCAUCC

TABLE D Primer Name SEQ ID Primer Sequence Primer Name SEQ ID Primer Sequence (target of PrimerC) F498 1746 GAGUGUGCGUGGCUCUCA R498 1275 UGCCAUCAUUCUUGAGGAGGAAG F499 1002 ACAACUGCAGCAAAGACUGGT R499 1276 UGCAAUCCCUGCCCCGGUT F500 1003 AGUUAAUUUUGGUUACAUCCCUCUCUGC R500 1277 GGAUUGCAGGCUCACCCCAAT F501 1004 AUCGAUCUGUUAGAAACCUCUCCAG R501 1278 CUGGAUUUCCUCAUGGAAGCC F502 1005 GGACUCUGUAGGCUGCAGT R502 1279 AAAUCCAGUUCGUCCUGUUCA F503 1006 UGAGGCAGUCUUUACUCACCUG R503 1280 GAAACUGCCUCUUGACCUGUCC F504 1007 ACAAGCAAAGUCUCUAUGGUGAUUAUGT R504 1281 AGGACAGUCAUGUUGCCAGUAUUAAAAT F505 1008 CAACUACCAUCCAGCAACAGAAAAT R505 1282 CUUCCAUGACUUUGGCAAUCUGG F506 1009 GACAGAUGAGAGAAAUGCACUUAGAAGA R506 1283 GAACAUGUCCUAUUUGAAUUUUCCGACUT F507 1010 AGGAAUGUGUUUCUCCAUACAGGUC R507 1284 GACACAAAGACUGGCUUACAUUUUGAT F508 1011 CUUCAAGCAGUGAGAAUACGUCCA R508 1285 AGGCUGACCACUUCUACUCUGT F509 1012 AGGGUCCAGGUUCUUCCAGA R509 1286 GCACUCAGGCUGGAUGAACAA F510 1013 GAUAGUUUUGAGAGUCGUUCGAUUGC R510 1287 UGUCCAGGGCUAUCUGGAAGAUC F511 1014 CUCCACCACCUCCUCAAACAG R511 1288 GCAGCAUUUACUGCAGCUUG F512 1015 AUCAGCCAGGCACAAAGC R512 1289 UGACAGAAGUACAUCUGCUAAACAUGA F513 1016 CAUCUUUGUCAUCAGCUGAAGAUGAAAT R513 1290 CUCACAGGAUCUUCAGCUGACC F514 1017 GCCUAAAGAAUCAAAUGAAAACCAAGAGA R514 1291 ACUUUGUUGGCAUGGCAGAAAT F515 1018 GUGACCCGGAGCACUUCC R515 1292 GCCGUGGUGCUGACCAT F516 1019 CCACAUUACAUACUUACCAUGCCACT R516 1293 GUGAUGAUUGGGAGAUUCCUGAUG F517 1020 AUGGGACCCACUCCAUCG R517 1294 GCUCUGAUAGGAAAAUGAGAUCUACUGUT F518 1021 CCCUUCUAAGGACCCCCUCUUC R518 1295 CUCCAGCAGGGCUUCGAT F519 1022 CUCUGCCGGGCUUUGAUCUT R519 1296 GGACUUUGCAACUUCAACAAAACUC F520 1023 UACUACCGCCUCACACGCT R520 1297 CUAGGUGUCUCCCCCUGUAAG F521 1024 UUCCCUCUCUCCUUCUGCCUC R521 1298 AGGUUCAGGCCUUGCACT F522 1025 CCAGCAGAAGACAAAAAGACAAACA R522 1299 CCAGCCCAGGAAGCAAAGAG F523 1026 GGAGAGGGAGGAGAGCUAACT R523 1300 UUAAAACUGGUCUCGCUCUCCC F524 1027 AGAAGCUGUGCAUUUACACCGA R524 1301 GAAAGCGGGAAUCGCAGAAA F525 1028 UUUUGCUGAUGCUAUGCUCUCCAC R525 1302 GGAAGACCUCUUCUUCGCACUT F526 1029 CUGAUCCGCAAGCAUGCUC R526 1303 CAAAAGAGCUCCCCCAUCUCC F527 1030 UGAGCUCGCUCACUUGUGAUG R527 1304 AGAAGAGACAUCUGGACUUAGCCAA F528 1031 CAGGAUCCAAAUUCGUUCUGUGC R528 1305 AUCAUCGACGGUGGGUACAUG F529 1032 UACUAACAACUCUGGUCUGGACCAT R529 1306 CGUUGGUCCUGACGGUACUG F530 1033 AUGCUAUUUGGACAAUAAACUCACCUUG R530 1307 CCAUUCUGAGGACUGCUGGUUUAUA F531 1034 CUCCUUACCUCAUACAGUGCAGAAA R531 1308 CCAGGACCAUCAUCCUACUGUAA F532 1035 CCCUGAGUGCAGCUUCGAUC R532 1309 GAGUGUUUGCUCCUCACUCUUC F533 1036 CGAUCAUGGAUGGCGGGUAC R533 1310 CUUCAGGUUUCCUUCUCUCAUGGUT F534 1037 UUUAUGAAUGGAGAGGCUGCUG R534 1311 GGAUGAGCUCACAGAGCUGC F535 1038 ACCUCUCACCCUUAUAAGUCUUCUGA R535 1312 UCAAAAAGCAUGCCCAGACCUUT F536 1039 ACUUGAGCUUCCCUAGGACCA R536 1313 ACUUUGAGACUUCUGCUUUGCUC F537 1040 GGGAGACAAUACGUGUCGGG R537 1314 AUCGAAAAACUGUGCAUCUACACC F538 1041 AAGACAGGUAGCGAUCCAGGUAG R538 1315 AGACCCAGCAGUGACUGT F539 1042 CUAGGUGCCCAUGUCCAUCUG R539 1316 ACAAGUAUAAUGAGCACCCCUUCT F540 1043 GAUGUCCAAUGUACCUGAGGCAA R540 1317 GUGGACACACCUGUAUUCCUGAG F541 1044 CAGCAGAAAGAGGACUCAGAAUAGAAAAUC R541 1318 CCGACCAGUUGGGCAAAAUC F542 1045 AGAGAUUCGCUUGUGUGGGUUAAA R542 1319 GCAGAAGUCUGUUUUCUUCAUGGUT F543 1046 ACCAGGGUUACCUUGAUCUCC R543 1320 AGGCCAUGUUGGGUUAAAGG F544 1047 ACUUCUCAAUUGCUACGGGCAAUC R544 1321 AGAAUCUACAGCUACCAGAUGGCA F545 1048 AGAUCUCGGUGAACGAUGCAAT R545 1322 CCUAGUUUCCAGUGCAUCUGUACC F546 1049 UAUGUGGACUGCAGAAGAACUUCG R546 1323 GGUCCCCAUCCAUUCUUCCUAUUC F547 1050 UGUGGUUUAUGAACAAGCGAUUUGG R547 1324 UGUGGAGUGUUGGCUGUAUCUUUG F548 1051 GCUCAUAUCGAGAGGUAGCCAUUC R548 1325 CUCUGUAAGCGACUUUUGGUGAUAG F549 1052 GCAGACGAGCUUGACAUCAGAAA R549 1326 GCCCAACCAAUUGAGAAGUUUGUAA F550 1053 AAGACUUCGGGUGCUCUGUAC R550 1327 UUAGUCAGGAGUCUAAGCCAACAG F551 1054 GGGACAGACUGUCAUUCAAAAUAGGA R551 1328 CUUGCCCGCAUCUAUAGUUUCCA F552 1055 UGAAGAAAGUCCAGACCUCGGA R552 1329 AACUUCCGUUUUGAGUGUUUACUGAUUT F553 1056 GUCGACUGCCUGAUAAGACAUGA R553 1330 UUACUUGGAUAAAGUUCCAGAGCCT F554 1057 UAGUUUGGUUUCUCUGUCUGUUCGUG R554 1331 GCUUAUUGCCACCUACUUAACCUCT F555 1058 AAGCCUCCAUCGCUACCCT R555 1332 CUUCAGCCCUGCAGGGAAA F556 1059 UCAGGCGCCAAGUAGGT R556 1333 GGCAAGUUCAACAUUAUUCCCUUUUGUA F557 1060 AAAGCGGCUGUUAGUCACUGG R557 1334 UCUUCCUCAGGAUUGCCUUUACC F558 1061 UAAAGAUCAUGUCUCGGCUCAAGGA R558 1335 CAUACAGAGAGGGUCAUCAGUGAUAC F559 1062 GUGCACAGGUUAUUCUGAUUUCCC R559 1336 GAAAGUCUCCCACAAAGUAACCC F560 1063 AGAAGGGCUAGGCCAAUUGAC R560 1337 AUAGUCAUAGCCGGGCCACA F561 1064 GUCAGCCUGAACAUAACAUCCUUG R561 1338 CCAGUUUAUUGUAUUUGCAUAGCACA F562 1065 GGGACCUCCGGUCAGAAAAC R562 1339 GGACCCAUUAGAACCAACUCCAUAAA F563 1066 CUCCCAACCAAGCUCUCUUGA R563 1340 UACCUUAUACACCGUGCCGAA F564 1067 CCCAGAAGGUGAGAAAGUUAAAAUUCC R564 1341 CCACACAGCAAAGCAGAAACUC F565 1068 AGGGCAUGAACUACUUGGAGG R565 1342 UUCUUUCUCUUCCGCACCCA F566 1069 GCCUCUCCCUCCCUCCAGGAA R566 1343 GUGAGGCAGAUGCCCAGCA F567 1070 UGCCUCACCUCCACCGT R567 1344 CCAAUAUUGUCUUUGUGUUCCCGGACA F568 1071 AAGUGUAAGAAGUGCGAAGGG R568 1345 UGUGUUCCUUUGGAGGUGGC F569 1072 GCCUUUUUAACUGGUAGAGAUUGGUG R569 1346 GAUCCAGAGGAGGAGUAUGUGUGA F570 1073 UCAUCACCUUCCUUUCAUGCUCUC R570 1347 UCUUCCUCCAUCUCAUAGCUGUCG F571 1074 UCCUACGUGGUGUGUGUCUGAA R571 1348 CGUCCUGUUUUCAGGCCAAG F572 1075 UGAUCAUCGAAUUCUCCAAAAUGGC R572 1349 AUUAGAGGGACUCUUCCCAAUGGA F573 1076 GAUGAGAUGUGGUACAAGCAUUCCA R573 1350 CCACGGUGGAAUUGUUGCUG F574 1077 CCCCUACAGCAUUGUUAAGAAAGUAUUT R574 1351 AUACCAGGCUAGUAUAGAUGCUUAGGG F575 1078 CUGGGACUAGCAUGCUGACC R575 1352 CAGACACCAACUCCCGGAAUC F576 1079 CUGCCUGUCUCUGGUUCUGT R576 1353 CAGAACUCUCUCCCCAGCAG F577 1080 ACUUGGAGUGAGUUUGGAUGGG R577 1354 CAGCUUCAUGUCUGUGCCG F578 1081 UCCUGAUCUCCUUAGACAACUACCUT R578 1355 UCACACCGCUGUGUUCCAUC F579 1082 UGUUCCUAUUUCAGCCCCACUC R579 1356 GUUGUGAGCGAUGAGCACGUA F580 1083 GGAAAGGGUCCUCUGAUCAUUGC R580 1357 AAAAUCGUGUCCUGGUAGCAGAG F581 1084 CGAGGGCCGGUAUACAUUCG R581 1358 CCCACCAAAAUGAGAAAACUGUGUT F582 1085 GAAUGUGAAAAUUCCAGUGGCCAT R582 1359 UGUCCUCCUAGCAGGAGAGG F583 1086 AUACCCUCUCAGCGUACCCUT R583 1360 CCGUGGAUGUCAGGCAGAUG F584 1087 AGCGCUUUGUGGUCAUCCA R584 1361 AUACUGGACUCAUCUCUCCUUCCC F585 1088 AAACUAGCCCUCAAUCCCUGAC R585 1362 AAAGACCACCCCCAAGACC F586 1089 CACAGUUGGAGGACUUCCUCUUC R586 1363 AUAACUCCACACAUCACUCUGGT F587 1090 CUACAUGGGUGCUUCCCAUUCC R587 1364 UUGACAUGGUUGGGACUCUUGAC F588 1091 GUCCUCGUGGCCAUGAAUGAA R588 1365 UGGCAAACUUCCCAUCGUAGAC F589 1092 CCCAAUCCCCACACCAAGUAUC R589 1366 GUUGAUCAUUGUUCCUUCCCCUCA F590 1093 AUGUUCCUCCCUCAUCUCUAAUGGT R590 1367 CCAUCUUGUCAGGAGGACAGG F591 1094 UGGACUCGAGCAACAUUGAUGG R591 1368 GGCAGGAUCUCUAACCCAUUGAG F592 1095 GCUGAAGUACCAGACCUGCUA R592 1369 CUCAGCAGGUAACUCACACUUG F593 1096 GGAUUUGACCCUCCAUGAUCAGG R593 1370 CUUCCCUGGGUGCUCCAT F594 1097 UCACUCUCUCUCUGCGCAUUC R594 1371 GUGGAUAUGGUCCUUCUCUUCC F595 1098 CAUGAAGUGCAAGAACGUGGT R595 1372 GGCUAGUGGGCGCAUGUAG F596 1099 GCGGAUCAGAGCCUCAAAC R596 1373 AUCAAAGUCCAGCACCAGCA F597 1100 ACUGUCCUGUUUUGAUAUCCCAGAUUUT R597 1374 GGGAAUUGCAUUCACACGUUAACA F598 1101 CUGUCUCAAUAUCCCAAACCCUAAG R598 1375 UUUGUUUUGUUUUUCUGUUUCUCCCUCUG F599 1102 UAUUAGUAUGCCCCUGCAACGUG R599 1376 GAGGGUUGUUAGUGGAGCAUAUGA F600 1103 CAACCCUCCUGCCAUCAUAUUGA R600 1377 UGAGACAGGCCAGUGUUUACAUG F601 1104 CAACCAUGACAAGAUUUUCCCUUACC R601 1378 GAGACUGGAGAAUGUAUACACACCUT F602 1105 UGCCUGUGGAGGAACUUUUCA R602 1379 CGACAUCUCCUCGGGCUT F603 1106 CUUCCUCUCGCCCAUCACA R603 1380 CGUAGAGCUCCGGGUGUC F604 1107 AGUGCCUCCUCUCCCAUCUT R604 1381 CUACCCAGGGCCACUGUUUT F605 1108 CACUCCUUGCUUCUCAGAUGAAACC R605 1382 GGGACAUUCACCACAUCGACUA F606 1109 CAGGUACUCCCGCAGGUUG R606 1383 UGGCCUCUUCUCCUGUGC F607 1110 CACGCAUACGGUUUGGUUUGG R607 1384 CUUCUUCUUCCCAUAGAUGCUCUCC F608 1111 CUAGAAGCUCUCUAUCCCACACCT R608 1385 GAGGCAUUAUUUGACCGGAUCUAC F609 1112 CAAGGAAUGCCUUCAAAAAGUUGGG R609 1386 CUGAGUAUGAGCUUCCCGAAGAC F610 1113 AGAUGAUGAUCUCCAGGUACAGG R610 1387 CCUGCUAACACCCUGUUCG F611 1114 CGGCACUGCAUGCAAUUUCUT R611 1388 CUGCCUGUCUCUCUUGGCUUT F612 1115 CCAUUUAUAGCUGAGUCUCCAUCCUG R612 1389 UAUGAACUUCCAGAGGACCCAAAAUG F613 1116 CCCAGUUGUGGGUACCUUUAGAT R613 1390 GGAAAAGAACGGCAGUAAAUACGG F614 1117 CUUUCAAACGAGUCAAGCAAGAAUGG R614 1391 AAUACGGGUCCAUCAAUCACACG F615 1118 ACCACACUUUCCAUAAUGAGGCT R615 1392 CAGUACUUGGUAUUCUGUGCUAGGA F616 1119 CUUUUCCAUCUUUUCUGUGUUGGUC R616 1393 GGAAGCUGUCCAUCAGUAUACAUUC F617 1120 CAGACAAAUCCCAAAACAAACCUGA R617 1394 GGCCCUCCUUCAGUUUAGUUGAG F618 1121 GUAGCUACAGGACUCAGAUACGUG R618 1395 GGUGGAGGCGAUAGUGGAUAG F619 1122 GUAUUUGGGCGAAUGCAGUUUUUC R619 1396 AGAUGGAGAUGAUGAAGAUGAUUGGG F620 1123 CCAGAGAAAAGAGAGUUACUCACACA R620 1397 GUCAAGUGGAUGGCUCCAGAAG F621 1124 ACUGUGUUACUGCCAUCGACUUAC R621 1398 CCAGAAAUGUUUUGGUAACAGAAAACAA F622 1125 GGUAUUCUCGGAGGUUGCCUUT R622 1399 AUUCUCUCUUUAGGGAGCUUCUCUUC F623 1126 CUUGGUCGUGUUCUUCAUUCGG R623 1400 UGGAAGAGAAAAGGAGAUUACAGCUUC F624 1127 ACCACUGUGGAGGCAUUUG R624 1401 AUUGGUCUCUCAUUCUCCCAUCC F625 1128 AGUGAAGAUCUCCCACAUUAACACC R625 1402 GUUUAGGUUUUGGCAACGUGGAT F626 1129 CUUGCCCAAAGCAACCUUCUC R626 1403 UCACCAGAUGCUAUGUGCUAAUCC F627 1130 AUUGGUUGCGGCCAUCUCT R627 1404 UCCUACCUGUGUCCACACC F628 1131 ACCAAUUUCAUAGGCGUGGC R628 1405 GGCAUGGGACAGAGUCGUT F629 1132 GCCUAUCGCUCUGCUCUCUC R629 1406 UUGUGCAAGGAGAGAACCUCUA F630 1133 UAACCCAGCGACGAACUUUCC R630 1407 CCUAUCCCAGAACUGGAGACAGAAA F631 1134 GCCCCUGAGCGUCAUCUG R631 1408 UGUACACCUUGCAGUGGAACT F632 1135 CUGGUGGAGGCUGACGA R632 1409 AGCCCAGGCCUUUCUUGG F633 1136 ACAACGUGAUGAAGAUCGCAGA R633 1410 ACUGGCAUGACCCCCAC F634 1137 GGGAGAUCUUCACGCUGGG R634 1411 UGCCACUCACAGGUCGT F635 1138 GUCUGAGGAGCCCGUGT R635 1412 GCAGAAACUCCCGCAGGT F636 1139 UCCUCGGAGCAGUGAGGG R636 1413 ACUCCAGAUACUGCAUGCCT F637 1140 AGCCUCUCCACGCUCCCUC R637 1414 ACUCCCGCAGGUUUCCC F638 1141 CUCACAUUGCCCCUGACAACAUA R638 1415 ACGGGAAAGUGGUGAAGAUAUGUG F639 1142 GUGUCCUUUCAGGAUGGUGGAUG R639 1416 AGAAACAUGAUGGAUGUCACGUUCUC F640 1143 GGUGACAUUUUCAAAGCAGUGUAUCC R640 1417 UGUUAACCUUGCAGAAUGGUCGAT F641 1144 GGGUAUUCGAUGAUCCCUGUGG R641 1418 AUGACUUGGACCGCGUAGC F642 1145 CCUCCCCACCAGCAUGUUT R642 1419 GCAUCCUACCGUUGAAGCACT F643 1146 GGCUUUGGUGAGAUCCAUUGAC R643 1420 CACCUGGAACUUGGUCUCAAAGAUT F644 1147 GCAUGUACUGGUCCCGCAT R644 1421 AUUCCUACCGGAAGCAGGT F645 1148 UGGUUCUGGAUCAGCUGGAUG R645 1422 AUGACGGAAUAUAAGCUGGUGGT R646 1149 UGCCAACAUGACUUACUUGAUCC R646 1423 AAAAUAUCCCCCGGCUUGUGAG F647 1150 GGACUAGGCGUGGGAUGUUUUT R647 1424 GAAGAAGAUGUGGAAAAGUCCCAAUG F648 1151 AGUGGAUCCCCUCUCCACC R648 1425 GUCCCUGGCUGGACCAA F649 1152 GAGGUUUUCCAGCACUCUGACAUAT R649 1426 CACACAUUGGAGCAUGCCAUUC F650 1153 CGGUUGAAUGUAAGGCUUACAACG R650 1427 AGCCUAAACAUCCCCUUAAAUUGGAUT F651 1154 GAACGGGAAGCCCUCAUGUC R651 1428 CGGCUUUACCUCCAAUGGUG F652 1155 CCUUACUCAUGGUCGGAUCACAAAG R652 1429 GCAGAGAAUGGGUACUCACGUUUC F653 1156 CCCUUUCUCCCCACAGAAAC R653 1430 UCAGCCUGUUUCUGGGAAACT F654 1157 GUAGAGCAAAUCCAUCCCCACA R654 1431 UGGAGAGAGAACAAAUAAAUGGUUACCUG F655 1158 UGUGCUUUUAGGGCCCACC R655 1432 GAUUCUUAUAAAGUGCAGCUUCUGCAT F656 1159 UCUGUUCAAUUUUGUUGAGCUUCUGAAUT R656 1433 CAGACGUCACUUUCAAACGUGUAT F657 1160 UCAGUGUUACUUACCUGUCUUGUCUUT R657 1434 CAGGCUCAGGACUUAGCAAGAA F658 1161 UGAAUUAGCUGUAUCGUCAAGGCA R658 1435 UAAGGCCUGCUGAAAAUGACUGAA F659 1162 UGUUUCUCCCUUCUCAGGAUUCCUA R659 1436 AGUCCUCAUGUACUGGUCCCT F660 1163 AAACCCGCAAUCCGGAAC R660 1437 CUGAUCUCGCCAUCGCUGUA F661 1164 CCCUCCAACAUCCUAGUCAACUC R661 1438 GUUCAUACCGACAUGUAGGACCUT F662 1165 GCUAGAGCUUGAUGAGCAGCAG R662 1439 UCAAAGUCGUCAUCCUUCAGUUC F663 1166 CCAUGGAGUCGAUGAGCUGG R663 1440 CCUCCAGAUGUGAAGCCCT F664 1167 GCCCAGCUCUGAGAUCCUUUC R664 1441 GCUGGAGGAGCUGGAACUT F665 1168 CAUUUCUGACAACUGAACUGCUCUC R665 1442 UAAACAGGAGCACGAGGAUGC F666 1169 UUACCAGCUUGUUCAUGUCUGGAUUC R666 1443 UAUUCAUCACGGCGCGCUT F667 1170 ACUGAGCUUGUUGGAAUAAGGAUGUT R667 1444 GAGUCCAGGAGAAAAUUCACAUGAGG F668 1171 UUGUAAGUGCCCGAAGUGUAAG R668 1445 ACAACCCACUGAGGUAUAUGUAUAGGUAUT F669 1172 UACGCAGUGCUAACCAAGUUCUUUC R669 1446 AGCACAGUGAAUUUUCUUGCCAUC F670 1173 CAGUCAAGGUUGCUGAUUUUGGUC R670 1447 GGUGGUAAACUUUUGAGUUUGCAGA F671 1174 UAUGGAUGUUGCCAAGCUGUAUUCUG R671 1448 GGGAAGGAGUGGUACAACAGAT F672 1175 GGUGGUCCUACCAUACAUGAAACAT R672 1449 ACAGCUAGUUUGCCAGUUAGUAAGC F673 1176 GCAAGCAAAAAGUUUGUCCACAGAG R673 1450 CACUUAAUUUGGAUUGUGGCACAGA F674 1177 ACAUCUCUCACCUCAUCUGUCCT R674 1451 CUCUUGUCAUCAGCUCCCAGA F675 1178 UCCCUGUAGUCCCGGAUGAG R675 1452 GCGCCAGCAUCCAGAGAUAC F676 1179 AAUUGUUGCCAUUUCAGGGUUUCUG R676 1453 GAGCGUGUGAUGCAGCUCUT F677 1180 CUCACCUAUCUCCCAGGCCUAAAAUA R677 1454 GUUUGACCGAAGAACCAAUUAUACCC F678 1181 ACAAACGAGAUGCCUCUUCCAG R678 1455 GAUGCUUCUCUCCUUCUUCUCUUGG F679 1182 GGCUGUCGUGGUAGACUUAGA R679 1456 UUCCCCAACCCACAUUUCCUUUAUAG F680 1183 CUGAGUGUAUCCUGGAGGUUGUUG R680 1457 CCAAAACCCUCCUGAUGUACACG F681 1184 GCUUGGUUCUGAUGUUUGUAGUGUAG R681 1458 GUCACAGCUCCAGUGUCUGUC F682 1185 UCCUUGUUGGUGUCCAUUUUCUUGT R682 1459 GAGAUCCAGGCUACCUGGUAUGAG F683 1186 ACAUGCCAUCAUUCUAGGAAGCUC R683 1460 AAGGACGACCCAGAGCUGAT F684 1187 CAGGACCCGCUUCUCUGAAAG R684 1461 AAAUUAAAAGGCAAGUGGACUUCGG F685 1188 AAGACCCCUUUAACUCAAGACUGC R685 1462 CUGUUGGUGAAGCUAACGUUGAG F686 1189 UGCUCCAUGAGGAGACACC R686 1463 AAAAUGGGAAAGGUAUCCAGCC F687 1190 AAUGUAACCUUGCUAAAGGAGUGAUUUCT R687 1464 CCACAGAAACAACAUCGAUUUCUUCC F688 1191 AACUGGCAAAUAUAUCAUUGAGCCAAAUC R688 1465 ACAGGGAUGGUGGUGGUT F689 1192 GGUGUGAAAUGACUGAGUACAAACUG R689 1466 UUCUGGAUUAGCUGGAUUGUCAGUG F690 1193 AUGGUGAAACCUGUUUGUUGGACAT R690 1467 GGCAAAUACACAGAGGAAGCCUT F691 1194 CCUGCUCAUGGUCUUUGAGUAUAUG R691 1468 AUGUCUAUAGGGAAGGGAAGACG F692 1195 GCCACACGCAACUGUCUAG R692 1469 GUCGGUGCUGUAGAUAUCCCT F693 1196 GACAAUCCUUGCUUACCUGAGGAAC R693 1470 ACAUUGUCAAGUUCUAUGGAGUGUGC F694 1197 GCUCGGGAUCCAUAUGUGGUAAT R694 1471 CUGGCUGAAGGUGGGUUUGAUT F695 1198 GGCCCUAUACUUAGGCCCUUUT R695 1472 AAGUCACACGGCCCUCC F696 1199 AACUCACGGUGGCUGCT R696 1473 UUGUUCUCAUUGGCUUCAAAGAUCUUUA F697 1200 UGUCCUGGUCAUUUAUAGAAACCGA R697 1474 UCUCUUGGAAACUCCCAUCUUGAG F698 1201 UCUCAUGUCUGAACUGAAGAUAAUGACT R698 1475 UGAGCCCACCUGACUUGG F699 1202 UUGGUAGCUCAGCUGGACUGAUAT R699 1476 ACAUGAGAGCUUGUUUUUCACUGG F700 1203 AUGAAGCAGGCUGAUACUACACAG R700 1477 AGAGUGAUCUCUGGAUGUCGGAAUA F701 1204 UUGUGAAGAUCUGUGACUUUGGC R701 1478 ACCAGUGAGGGAAGUGAGGAC F702 1205 CCUUUGGGUUAUAAAUAGUGCACUCAGA R702 1479 UAAGCAUCAGCAUUUGACUUUACCUUAT F703 1206 GGGAAGAAAAGUGUUUUGAAAUGUGUT R703 1480 CAAACAAGUUUAUAUUUCCCCAUGCCA F704 1207 UGGCUUUGAAUCUUUGGCCAGUA R704 1481 GAUUUGAUCCAGUAACACCAAUAGGGUT F705 1208 GUCGAGGCAAUGGAAAAGCUC R705 1482 AAACACAAACUAGAGUCACACACCUT F706 1209 AGAACAGCUCAAAGCAAUUUCUACA R706 1483 AGCACUUACCUGUGACUCCAUAG F707 1210 AGCAAGAGGCUUUGGAGUAUUUCAUG R707 1484 UUGUGUGGAAGAUCCAAUCCAUUUUUG F708 1211 UGUUCAUGCUGUGUAUGUAAUAGAAUGUT R708 1485 AACCAUAUCAAAUUCACACACUGGC F709 1212 CUGGAAUGCCAGAACUACAAUCUUUUGA R709 1486 CUCUUGCUCAGUUUUAUCUAAGGCUAG F710 1213 CUCAAGAAGCAGAAAGGGAAGAAUUUUT R710 1487 CAUACCAAUUUCUCGAUUGAGGAUCUUUUC F711 1214 UGACAGCCAUCAUCAAAGAGAUCG R711 1488 CCGCAGAAAUGGAUACAGGUC F712 1215 GGGAUUUCCUGCAGAAAGACUUGA R712 1489 AGAAAAUCAAAGCAUUCUUACCUUACUACA F713 1216 AAGGCACAAGAGGCCCUAG R713 1490 UCCAGGAAGAGGAAAGGAAAAACAT F714 1217 ACCAAUGGCUAAGUGAAGAUGACAAT R714 1491 AUUUGCCCCGAUGUAAUAAAUAUGCAC F715 1218 AGGUUAUCUUUUUACCACAGUUGCAC R715 1492 GUCAAGAUCUUCACAAAAGGGUUUGA F716 1219 UUUUCUGUCCACCAGGGAGUAACUA R716 1493 GCCACUGGUCUAUAAUCCAGAUGA F717 1220 GACAAGUUCAUGUACUUUGAGUUCCC R717 1494 GCAUCUUGUUCUGUUUGUGGAAGAA F718 1221 AGCAAAUAAAGACAAAGCCAACCG R718 1495 UCAACAACCCCCACAAAAUGUUT F719 1222 AGUUUAAGAUGAGUCAUAUUUGUGGGUUUT R719 1496 UGGAUUUGACGGCUCCUCUAC F720 1223 CUGACCAUGUGGACAUUAGGUGUG R720 1497 UUAACACCUCCAGUCCCUCAUCUG F721 1224 CCUUCCCUCGGGAAAAACUGAC R721 1498 UAAGAUGUCCACUGCUGUUCCUUCAUA F722 1225 GUUUGGUUUUGUAGGUCUUGUGGAUG R722 1499 CUUCAGCCAAGGCAGCAAUG F723 1226 GAGGUGGCCUGAUCUUCACAA R723 1500 GAUAUGGAUUCACACAGACACUAUCACA F724 1227 CGCUUAUGCAUACUCAGGAUGAGUT R724 1501 CAAGGUGUUUCUUUGAUGCUCUGT F725 1228 UAAGGUUCCUUCAAGCUGCCCUA R725 1502 CCUGUGGACAUUGGAGAGUUGAC F726 1229 CAUGGGAGGAUGUUCUUUCCCAUUT R726 1503 GAACCUUAAAUGUCUCUCCUACCUGA F727 1230 UUUUCUUCCUAAGGUUGCACAUAGG R727 1504 AAGGCACCUGACCCAAACA F728 1231 AUUUUUGGCUUCCUGGCCUUT R728 1505 GCACAUAGUCCCGGAAGCUG F729 1232 GGAAAGCCUCACCUGUCUACG R729 1506 UUCUUGAUCUCACAGUCAGGGAUG F730 1233 UCAAGAAUCGCCCGAGCC R730 1507 AUGAGCAGCGUGGCCUT F731 1234 UUGGUUCGGACAGACAACCC R731 1508 UAGCUGUGCAUGUCCUGGUG F732 1235 CUCUGCACAGCUCCAAUGAGAC R732 1509 UAGGUGAGGACCACAAACCAAAC F733 1236 GCUACAAGAACUACCGAUACCGT R733 1510 UGGUCUUCACUCACCUCGGAT F734 1237 CUCGGAGAGGAGCCAUACUG R734 1511 UUCCUCCAGAAGCUUGAACUCT F735 1238 UAUAAUGACAGUUAACCCUGCCAGGA R735 1512 CCCAAGCCUGGGACCUCUAUUAT F736 1239 AGGAAGAGCACAGUCACUUUGA R736 1513 CAUGCUGGACCUUCUGCAC F737 1240 CAGUGGAGCGAAUUCCUUUGGA R737 1514 AGACUGCUAAGGCAUAGGAAUUUUCG F738 1241 UUGGGUCGUUGGGCAUUCC R738 1515 UUUGACUCUGUCUCCUCUUGUCUUCT F739 1242 CAGUUCACAGUGCAGCGAAAA R739 1516 GAGAUGAAGCAAACAACAGUGGAG F740 1243 AAAUAUCUACACACAGGUCUACAAGGUC R740 1517 AUUUCAUGCAAACUAGAUAACUACCUGUAA F741 1244 CAUCCGGGCUUUACGCAAAUAA R741 1518 UGGAGUUUGUCUGCUGAAUGAACC F742 1245 GCCUCCUUCAGGAAUUCAAUCUUCT R742 1519 AGCUCACAGAAAUGUCUGCUAUACUG F743 1246 AUGAGUUCUGGGCACUGGG R743 1520 AUGAGGAGUGUGUACUCUUGCAUC F744 1247 GAUGCAAACUCUUGCACAAAUGCT R744 1521 GCCAAGAGUUACGGGAUUCCAT F745 1248 GAACCCCGAGGGCAAAUACAG R745 1522 AGGAUGCCUGACCAGUUAGAGG F746 1249 CAGUUCGUGGGCUUGUUUUGUAUC R746 1523 AAAAGACUCGGAUGAUGUACCUAUGG F747 1250 UUAAAGCUGGCUAUGGCACCUG R747 1524 CACUCACCCUGGAUGUCUUCG F748 1251 CAUCUCUCACCAUCCCAAGG R748 1525 CACCGUAGCUCCAGACAUCA F749 1252 AUACGCAGCCUGUACCCA R749 1526 AAGGAGAAGAGGACAGCGG F750 1253 CACCUCUCUCAAGAGUUUGGAUGG R750 1527 CCUGCACUUCUAGGCACUUACUAA F751 1254 AGAUUGCGAGAGAGCUGCAT R751 1528 GGCACUUGCACAGAGAUGAT F752 1255 CUGUGCUGCAUUUCAGAGAACG R752 1529 AUUUGAUGACAUGUGGGUGGUUG F753 1256 AAGACCCAAGCUGCCUGAC R753 1530 GGAGCCGUAUUUGGCGT F754 1257 GCUAUUUUUCCUCACAGCUCGUUC R754 1531 CCUCUUCACGUAGGAAUCCUCUUC F755 1258 CUCCUUCCUAGAGAGUUAGAGUAACUUC R755 1532 AUCACUUUGCGUGGUGUAGAUAUGAT F756 1259 GAGCCUGUUUUGUGUCUACUGUUCUA R756 1533 AGGACUCUGAAGAUGUACCUAUGGT F757 1260 CUCUUGCAGCAGCCAGACT R757 1534 ACAGUUUCCAUAGGUCUGAAAAUGUUT F758 1261 CCAUGGGACUGACUUUCUGC R758 1535 AGCCCAACCCUUGUCCUUAC F759 1262 GCUGAGGACCUGGUCCUCT R759 1536 GGGACAGCAUCAAAUCAUCCAUUG F760 1263 CUGCACCAGCAGCUCCUA R760 1537 CCAGACGGAAACCGUAGCUG F761 1264 CCCGGACGAUAUUGAACAAUGGT R761 1538 GGAGCAGCCUCUGGCAUT F762 1265 AGCCUCACCACGAGCUG R762 1539 GGCAAGGAAAGGUGAUAAAAGUGAAUCT F763 1266 CACCUUUCCUUGCCUCUUUCCUA R763 1540 ACUUGAUAAGAGGUCCCAAGACUUAGT F764 1267 CUCAAGGAUGCCCAGGCT R764 1541 CCUAUGGCUUUCCAACCUAGGA F765 1268 CCUCCCUGCUUCUGUCUCCUA R765 1542 CCCUUCUGUCUUGAACAUGAGUUUT F766 1269 CCAGUUGCAAACCAGACCUC R766 1543 UGUGGAGUAUUUGGAUGACAGAAACA F767 1270 ACUCCACACGCAAAUUUCCUUC R767 1544 AGGCCUCUGAUUCCUCACUGAT F768 1271 AGGGUGGCAAGUGGCUC R768 1545 CCUAGGUUGGCUCUGACUGT F769 1272 GAGGCUCCCCUUUCUUGC R769 1546 UGCCUCUUGCUUCUCUUUUCCT F770 1273 CUGUGACUGCUUGUAGAUGGC R770 1547 UUCCUACAGUACUCCCCUGC F771 1274 CUGUCGUCUCUCCAGCCC R771 1548 AGUCACAGCACAUGACGGA F772 1549 GGAGGAGGCGAUGGCUACUA R772a 1574 CUGCAGUUAGAGGUUGGUGACA R772b 1575 CCCGCCAAGCACGUAUACU F773 1550 GGAGACCUACAAACUGAAGUGCAA R773a 1576 CCGGAAGAGGAGUAGCUGAC R773b 1577 CUCCUAGAGUUUUUCCAAGAACCAAGU F774 1551 CCAUGCAGAAUGCCACCAAGUA R774 1578 AUUUGCAGCUACUACUCUGAACUGAA F775 1552 CAGGCACUCCUUGGAGCAA R775 1579 UCAGUGGGAUUGUAACAACCAGAAAU F776 1553 CUGUUUGAAAUGAGCAGGCACU R776 1580 GCACUGUCACCCCUUCCUUG F777 1554 ACUGGAGGACCCGUCUUCU F778 1555 AGACCUUAAGGGAACAGCUCUCAU F779 1556 GUGGAGUCAUGCUUAUAUGGAGCAAA R779 1581 GCUCCAUCUGCAUGGCUUG F780 1557 GACAGAAAAAUAAUUCUGUGGGAUCAU F781 1558 UCCUGAAAGAGAAAUAGAGGUUCCUGAU F782 1559 GGTGGCCATAGGAACGCA F783 1560 UGGAUGCAGAAACCAGAGAUCUAGU F784 1561 CUGGUCCCCAGACAACAAGUAU F785 1562 GAAGAUCAUGUGGCCUCAGUGAA R780 1582 GGGUUGUAGUCGGUCAUGAUGG F786 1563 GUCGAAAAUACCUUCAACACCCAAAUU R781 1583 CCUGGCCCUUGAAGCACUA R782 1584 ACCCCAUCUUCCCCAUCCAU F787 1564 CCAAAACUGCAGACAAGCAUAAAGAUG R786 1585 CUACCUCACAGUGACUGCAGUUUA R787 1586 AGAGAGGAUCAGCGAGAGUGG F788 1565 CAGGCAGAAGUUGAUCGACUCU R788 1587 GUCUCGUUGCCCAAAUUGAU F789 1566 AAAGAAGAGUGCACAAAUGUUAGAGGA R789 1588 AGUGUUUUCAUUCGAUUCCUGUCUUCU F790 1567 CCAGCUUCCUAUAACUUGGACGAU F791 1568 GAACCACAUCAUGGUCUCUGUCU R791 1589 GGUGAUGCCGUGGUUGAUGU F792 1569 UCAUCGGGAAGACCUGGCUUA R792 1590 AGUUCUCGCUUCAGCACGAU F793 1570 GCUGCAGGACUAUGAGGAGAAGA F794 1571 CUCCCAGAGACCAACGUUCA R794 1591 UGGCCAAGCAAUCUGCGUAU F795 1572 GGACCUGGACCGUGUCCUUA R795 1592 UGCCAGGAUCAUAGCGUUUACAG F796 1573 GGACCUGGACCGUGUCCUUA R796a 1593 CUGGAGCAGGUCCACUAUAGGU R796b 1594 UCCUCACACCUGCUCCUCA R796c 1595 GCUGAUGGGUGGGCACUG R796d 1596 GGUCUACCAGGACUGUCCCU F797 1760 CCCUUCGUAGACAUAUAGCUGUUCUC R797 1597 GGAAGGCAGGAAGAUUUUCAAUCUC F798 1761 UGGUGCUAGUUGCAAAGACACAA R798 1598 CGUUUAUAAGCACUGUCACCCCUU F799 1762 AGCGACGCCAUUGCUCAU F800 1763 CCUCAACCAUUUCCGGCAAAU F801 1764 CCAGCUCCCUGCGAAGAG R801 1599 AGGAUGAUGGCACUGAACUCC F802 1765 AAUCCCUGCAGUAGAUACGAAGACUA R802 1600 CACGUUAGUUAGUGAGCCAGGUAAU F803 1766 AGACCUUGCAGAAAUAGGAAUUGCU R803 1601 CUCAGGGCUCUGCAGCUCC F804 R804 1602 CCUCCGGAAGGUCAUCUCA F805 1767 AAAGAAAAGACAGUUGGAGGAAUCUGU R805 F806 1768 GAAGAAAAUGAAAAGGAGUUAGCAGCAU R806b 1603 CUCCUAGAGUUUUUCCAAGAACCAAGU R807 1604 GAACCAAGUUCUUCCGAGGGAAU F807 1769 AGUGGCAAAAGAACUUCAGACUUUACA F808 1770 GCGCUGCUCAGAAGCAAAA F809 1771 GUAGAUCGCAUAAAGGAAGCAGUCA R809 1605 ACAGCGGCUGCGAUCACC F810 1772 GGAAGCAGUCAGGUCAAAGAAUAUGG F811 R811 1606 GCUGACUGCACAGGACAGG F812 1773 CAAGCAGAAACACUGUACAAAGAGAUU F813 1774 GAGGGCGAGCUGCAUGAU R813a 1607 CGAGACCCCAAAAGGUGUUUC R813b 1608 UCCACAUUUGUUGAGCACAAGGA F814 1775 CACAUCUUCAGGUGCUGGAUUUUUC F815 1776 CUUUUGAAAAGCCAGUGAUGAUCUCAA R815 1609 CACCUUUAACUGCUUCAGGGUCAAUAU F816 1777 GCACCUUGACUUUAAGUGAGAGCA R816 1610 UGUUGUCCCGUGGCCAUU F817 1778 ACAGCACUGUUAUUACUACUUGGGUUUU R817 1611 GGCAUGAACCGUUCUGAGAUG F818 1779 CAAGCUCCUUACAUACCCAGCA R818 1612 CCAAAUUCGCCUUCUCCUAGAGU F819 1780 GCGUUUCCUCGCUUGCAUU R819 1613 CUCCUCUGCACCAAGGUAAACA F820 1781 CGGGCAGGAATCTGATGACTTT R820 1614 UCCCUUCUAGUAAUUUGGGAAUGCC F821 1782 GCAGGGCAGCAACAUCUUUG F822 1783 GGCUCCUGAGACCUUUGAUAACAUAAC F823 1784 CGUGUGCUCCCUGGAUAUUCUUAGUA R823 1615 UCAGCUUUCUCCCACUGUAUUGAAUUUU F824 1785 CUGGCUCCGGGUGACAGC R824 1616 UCGGAAGGGCUGUGGAAUUG R824b 1617 CGUAGGCACACUCAAACAACGA F825 1747 CUGGCUCCGGGUGACAGC R825 1618 CUGAUUUCUGAACAUGGACUGUGG F826 1748 GACUCCCAUGACCCCCAUC R826 1619 ACGAAGUGCAAUGGUCUUUAGGU F827 1749 AAAAAUGUUAUGUCAGCGUUUGGCUUAA F828 1750 GUAGGCGCGAGCUAAGCA R828 1620 GUGAGUCAUUUGUCUUGCUUUUGGU F829 1751 CAGGUCAUAUUGAACAUUCCAGAUACCU F830 1752 GGUCCUGACGCAGGCUUC F829 1621 GACAGUCUGAAUCAUGUCCUUCAGU F830 1622 GGGCUGCCCACCAUCUUC F831 1623 UCAGCCUGAUAGUCUGGUACAAACU F831 1753 GUACCUGCAUCAACCCCUCUAA F832 1754 CAGAGACCCGUGCUGAGUUU F833 1755 GGAGAGAAGAGUGCACAAUACCA R833 1624 CCUCCACCUUGGGCUACUCA F834 1756 CCUGUAAUCCCUGCACUUUAGGA R834 1625 GGGUGAGCCUUGACACACA F835 1757 ACUUUCCAGUUGAGCAUCCCAAAUU R835 1626 CAGGGAUCAGUUCAGCUGUACC F836 1758 CGUCAGCGUGAUAUGUACCGUAUUUUAU F837 1759 CACCUCAGUAAUAUGGAAGUCCAAGUU

TABLE E SEQ Primer Name ID Primer Sequence Primer Name SEQ ID Primer Sequence F838 1627 UGGGCUCUGUAAAGAAUAGUG R838a 1665 AUCAGAGCUUAAACUGGGAAG R838b 1666 AUCAGAGCUUAAACUGGGAAA F839 1628 UGCACACUUGGACAGCAUUUC R839 1667 GUCUCAGUUUUCCUACCUGUAAAAUGAAG F840 1629 CCAGGACCAAUCUGGUCACAAACAUA R840 1668 ACUUAUUCUGACAGUUCUCUUUUUCCCT F841 1630 GGUGGGAGGAAAAGACAUAGGAT R841 1669 GGUGGCAGUGAGCUGUAACAGUA F842 1631 CUCCAGAGAGAAAGAAUCAACAGG R842 1670 UCAGCCUCCAUAUCACUUGAGC F843 1632 GCAUCCGUGACUCUCUGGAC R843 1671 AACUUGGGUUGAGCCAUAGGC F844 1633 UCAGUGAGCCAAUUCCUUGUAAUAACUC R844 1672 CCUGGUUCCAUGGAUUCCACAUUAAGA F845 1634 CAGAUCCCAAGCUCUUCCUCUT R845 1673 GCGUUUGUGUGUGCAUCUGT F846 1635 GUUCAUGCCACUGCACUUCACT R846 1674 UCUGGUGUGUGGAGAUGUCUUAC F847 1636 GGUGCACCCAUUACCCGAAT R847a 1675 GGCUGCAAAAAGCUAUAAUUGUACC R847b 1676 GGCUGCAAAAAGCUAUAACUGUACC F848 1637 UCCCCAUAUAAGUUCAAGCCUGUGT R848 1677 UGUGUUAGUCAGGAUUCUUCAGAGA F849 1638 UUGUAUAGCUACAGUUUUUCUGUUGGT R849 1678 UUCAGUUAUAUGUGUAUAAAUGUGUGCAUUG F850 1639 UAAAUAUGUGAGUCAAUUCCCCAAGUG R850 1679 CUCCAGAGACAGACUAAUAGGAGGUA F851 1640 GGCUAGAUUUUCCCCGAUGAUAGUAGT R851 1680 CCUGUGCCCAAGUUGAGAGAAT F852 1641 GGCUAGAUUUUCCCCUAUGAUAGUAGT F853 1642 CAGUAAGUUAAAGGAUUGCAGGAG R853 1681 UAAUCCAGCUGUGGGAGGGA F854 1643 UGUGUAUAUGCAUUUACCUGUGAGUAUG R854 1682 GGUGCUAGGUGUGCUCAGGA F855 1644 UGUAACAAGGGCUACAGGAAUCAT R855 1683 CUUCACUCUCCUUCCCAAAUGUUUAUG F856 1645 GGGCAUCUCUUAUACUCAUGAAAUCAA R856 1684 CUAUGAUUCCCCCACUGCAGUC F857 1646 CUAUGCAGAAGAAUGAACCAGGGAT R857 1685 AGACCCCAAAAUUACUUGAGCCAAUUUA F858 1647 UGAUUCAUUUCCAUAGGGUAAGUGAAAA R858 1686 ACUUCAACUUCAAUUCAUCCACUGAAA F859 1648 GACAUUAUCACCAAUUUUUCUAGACG R859 1687 UGCUUGCCUGUAUGAAAAUAUCUC F860 1649 GACAUUCUCACCAAUUUUUCUAGACG F861 1650 UGUGACAAGGGUGAUUUUCCUC R861 1688 UCCAAUCAUAGCCACAGUUUACAA F862 1651 CAUAAUUGUAUGAGCCACUUCCCAT R862 1689 GCACUCUUAUUCAUCUAGUUGCCUGT F863 1652 AGACUCACAAUGUACAAAAGCCUAUT R863a 1690 CAUCAUGUGAGCCAAUUCCUCUC R863b 1691 CAUCAUGUGAGCCAAGUCCUCUC F864 1653 AAUAUAUAUAAAGGGUAUGAUAGAACACUUGUC R864a 1692 UUGCACCAAAUAUUGGUAAUUAAAUGUUUACT R864b 1693 UUGCACCACAUAUUGGUAAUUAAAUGUUUACT F865 1654 GGCCUGGCAACUUAUAUGUAUUUUUGUAUT R865 1694 CACUGUAUCGUAUCCCAUUGCG F866 1655 GGCCUGACAACUUAUAUGUAUUUUUGUAUT F867 1656 CCAUCCUUAUCUCUUGUGUAUCUAUUCAUUCAA R867 1695 UUGCAAGCAAUUGCCAUAGAGGGA F868 1657 GAUUUGUCUGUAAUUGCCAGCAAAA R868 1696 ACAGAUUAAACUGUAACCAAAAUAAAAUUAGGC F869 1658 GAGCAAGACACCAUCUCAAGAA R869a 1697 UGCCUAACCUAUGGUCAUAACG R869b 1698 UGCCUAACCUAUGGUCAUACCG F870 1659 CAUGAUUGAUACAUGGAAAGAAUUCUCT R870 1699 CCCAGGAGGUGGAGAUUGAA F871 1660 ACCCAAAUCAACUCAACUCCAGUG R871 1700 UCCAUGUACUUUGUCCAAUGCUGA F872 1661 UUAGAGCAUUUAAAGUAAGCCACAGUGT R872 1701 UGUCAACACGAUUAACAUGCAAAGA F873 1662 CUGUACACAGGGCUUCCGAGT R873 1702 CAAAAUUCAAAGGGUAUCUGGGCUCT F874 1663 UUUCAGGGCUGUGAUCACUAGCAC R874 1703 UGUGCGCUGGUCUUACUCCUGUT F875 1664 AGAUACAUAGGUUAGAUAGAGAUAGGACAGA R875 1704 GCCCUAGUGGAUGAUAAGAAUAAUCAG 

What is claimed is:
 1. A method for preparing a library of target nucleic acid sequences comprising (a) contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; (b) digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and (c) amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; wherein each of the plurality of adaptors comprises a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences; wherein at least two and up to one hundred thousand target specific adaptor pairs are included; and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety.
 2. The method of claim 1 wherein an optional tag sequence is included in at least one adaptor, and the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.
 3. The method of claim 2 wherein all of the adaptors comprise tag sequences having cleavable groups flanking either end of the tag sequences.
 4. The method of claim 2 wherein each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences.
 5. The method of claim 1 carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries.
 6. The method of claim 1 wherein the digestion and repair of step (b) is carried out in a single step or is carried out in a temporally separate manner at different temperatures.
 7. The method of claim 6, wherein the plurality of gapped polynucleotide products in step (b) are contacted simultaneously with a digestion reagent and a repair reagent.
 8. The method of claim 6, wherein the plurality of gapped polynucleotide products in step (b) are contacted sequentially with a digestion reagent and a repair reagent.
 9. The method of claim 6, wherein a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase.
 10. The method of claim 9 wherein a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, and T7 DNA ligase.
 11. The method claim 1 wherein one or more of the method steps is conducted in an automated mode.
 12. The method of claim 1 further comprising at least one purification step.
 13. The method of claim 12 wherein a purification step is carried out only after step (c) or wherein a first purification step is carried out after step (b) and a second purification step is carried out after step (c).
 14. The method of claim 1, further comprising analyzing the sequence of the resulting library of target nucleic acid sequences.
 15. The method of claim 14 wherein analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing.
 16. The method of claim 15 wherein sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon.
 17. The method of claim 14 further comprising determining the abundance of at least one of the target nucleic acid sequences in the sample.
 18. The method of claim 1, wherein a digestion reagent comprises any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta.
 19. The method of claim 1 wherein a repair reagent comprises any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9° N DNA ligase.
 20. A method for preparing a library of target nucleic acid sequences comprising (d) contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; (e) digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and (f) amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; wherein each of the plurality of adaptors comprise a universal handle sequence, one or more tag sequences, a target nucleic acid sequence and a cleavable moiety; and wherein at least two and up to one hundred thousand target specific adaptor pairs are included; wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included in the flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety. 